rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 34960,SRR32588717,SRX27895234,SRS24266236,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F K,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from kidney,C2 F2 F K,C2 F2 F K,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240904_132604_s1.skera.flnc.fastq.gz,fastq,109258150145.0,61126158.0,m84270 240904 132604 s1.skera.flnc.fastq.gz,0:1787.42,A:32153042096;C:22604112467;G:23394852841;T:31106142741;N:0,1787,,,,32153042096,22604112467,23394852841,31106142741,0,SRX27895234,SRS24266236,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Kidney,Renal System 34970,SRR32588727,SRX27895224,SRS24266224,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 M K22,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from kidney,C2 F2 M K22,C2 F2 M K22,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240829_144745.hifi_reads.flnc.fastq.gz,fastq,14838539048.0,3383142.0,m64467e 240829 144745.hifi reads.flnc.fastq.gz,0:4386.02,A:4211191682;C:3185079857;G:3320422646;T:4121844863;N:0,4386,,,,4211191682,3185079857,3320422646,4121844863,0,SRX27895224,SRS24266224,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Kidney,Renal System 34971,SRR32588728,SRX27895223,SRS24266234,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 M K21,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:Kidney|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from kidney,C2 F2 M K21,C2 F2 M K21,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240913_170640_s3.skera.flnc.fastq.gz,fastq,100849133955.0,51593887.0,m84270 240913 170640 s3.skera.flnc.fastq.gz,0:1954.67,A:28887816631;C:21568633305;G:22323254809;T:28069429210;N:0,1954,,,,28887816631,21568633305,22323254809,28069429210,0,SRX27895223,SRS24266234,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Kidney,Renal System 38296,SRR1647681,SRX756916,SRS742120,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,24K,GSM1541905,,source name:head kidney|tissue:head kidney|disease state:24h post SVCV infection,24K,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,head kidney,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head kidney|disease state:24h post SVCV infection,GSM1541905,GSM1541905: 24K; Danio rerio; RNA Seq,GSM1541905,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541905,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,24K_GTGAAA_L003_R1.fastq,fastq,1020487560.0,20009560.0,GSM1541905 r1,0:51,A:266117014;C:246797067;G:240014464;T:267491299;N:67716,51,,,,266117014,246797067,240014464,267491299,67716,SRX756916,SRS742120,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.92411,,0.07686,,0.68647,,0.4627,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Kidney,Renal System 38297,SRR1647680,SRX756915,SRS742117,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,6K,GSM1541904,,source name:head kidney|tissue:head kidney|disease state:6h post SVCV infection,6K,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,head kidney,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head kidney|disease state:6h post SVCV infection,GSM1541904,GSM1541904: 6K; Danio rerio; RNA Seq,GSM1541904,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541904,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,6K_GTCCGC_L003_R1.fastq,fastq,929436036.0,18224236.0,GSM1541904 r1,0:51,A:242005719;C:225485975;G:219890494;T:241993975;N:59873,51,,,,242005719,225485975,219890494,241993975,59873,SRX756915,SRS742117,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.92547,,0.09105,,0.69264,,0.49166,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Kidney,Renal System 38298,SRR1647679,SRX756914,SRS742116,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,0K,GSM1541903,,source name:head kidney|tissue:head kidney|disease state:un infected,0K,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,head kidney,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head kidney|disease state:un infected,GSM1541903,GSM1541903: 0K; Danio rerio; RNA Seq,GSM1541903,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541903,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,0K_CCGTCC_L003_R1.fastq,fastq,1077979095.0,21136845.0,GSM1541903 r1,0:51,A:280277150;C:261348733;G:255721013;T:280562071;N:70128,51,,,,280277150,261348733,255721013,280562071,70128,SRX756914,SRS742116,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.92545,,0.08181,,0.68373,,0.49408,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Kidney,Renal System 47595,SRR6661145,SRX3638241,SRS2904492,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidWTPHZ 3,GSM2975189,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,KidWTPHZ 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,GSM2975189,GSM2975189: KidWTPHZ 3; Danio rerio; RNA Seq,GSM2975189,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975189,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidWTPHZ_3.fastq.gz,fastq,858099990.0,16825490.0,GSM2975189 r1,0:51,A:231903062;C:197865548;G:200825484;T:227491985;N:13911,51,,,,231903062,197865548,200825484,227491985,13911,SRX3638241,SRS2904492,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.9605,,0.10316,,0.70721,,0.51089,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47596,SRR6661144,SRX3638240,SRS2904491,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidWTPHZ 2,GSM2975188,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,KidWTPHZ 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,GSM2975188,GSM2975188: KidWTPHZ 2; Danio rerio; RNA Seq,GSM2975188,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975188,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidWTPHZ_2.fastq.gz,fastq,799571013.0,15677863.0,GSM2975188 r1,0:51,A:217401512;C:183178629;G:185275617;T:213702318;N:12937,51,,,,217401512,183178629,185275617,213702318,12937,SRX3638240,SRS2904491,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.96209,,0.10882,,0.70861,,0.5149,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47597,SRR6661143,SRX3638239,SRS2904490,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidWTPHZ 1,GSM2975187,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,KidWTPHZ 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,GSM2975187,GSM2975187: KidWTPHZ 1; Danio rerio; RNA Seq,GSM2975187,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975187,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidWTPHZ_1.fastq.gz,fastq,816038505.0,16000755.0,GSM2975187 r1,0:51,A:218420574;C:190260181;G:192288409;T:215056318;N:13023,51,,,,218420574,190260181,192288409,215056318,13023,SRX3638239,SRS2904490,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.96264,,0.09527,,0.70834,,0.51477,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47598,SRR6661142,SRX3638238,SRS2904489,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidWT 3,GSM2975186,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,KidWT 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,GSM2975186,GSM2975186: KidWT 3; Danio rerio; RNA Seq,GSM2975186,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975186,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidWT_3.fastq.gz,fastq,852094026.0,16707726.0,GSM2975186 r1,0:51,A:234167802;C:192807979;G:194651214;T:230453461;N:13570,51,,,,234167802,192807979,194651214,230453461,13570,SRX3638238,SRS2904489,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.95788,,0.12336,,0.70258,,0.48964,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47599,SRR6661141,SRX3638237,SRS2904488,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidWT 2,GSM2975185,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,KidWT 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,GSM2975185,GSM2975185: KidWT 2; Danio rerio; RNA Seq,GSM2975185,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975185,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidWT_2.fastq.gz,fastq,969772038.0,19015138.0,GSM2975185 r1,0:51,A:265582126;C:219526888;G:222468938;T:262178447;N:15639,51,,,,265582126,219526888,222468938,262178447,15639,SRX3638237,SRS2904488,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.95803,,0.12522,,0.69794,,0.50805,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47600,SRR6661140,SRX3638236,SRS2904487,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidWT 1,GSM2975184,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,KidWT 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type,GSM2975184,GSM2975184: KidWT 1; Danio rerio; RNA Seq,GSM2975184,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975184,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidWT_1.fastq.gz,fastq,815590011.0,15991961.0,GSM2975184 r1,0:51,A:224190865;C:184406547;G:186159880;T:220819162;N:13557,51,,,,224190865,184406547,186159880,220819162,13557,SRX3638236,SRS2904487,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.95883,,0.13181,,0.7023,,0.49523,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47601,SRR6661139,SRX3638235,SRS2904486,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidDKOPHZ 3,GSM2975183,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,KidDKOPHZ 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975183,GSM2975183: KidDKOPHZ 3; Danio rerio; RNA Seq,GSM2975183,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975183,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidDKOPHZ_3.fastq.gz,fastq,789588885.0,15482135.0,GSM2975183 r1,0:51,A:215354577;C:180286176;G:181162894;T:212772248;N:12990,51,,,,215354577,180286176,181162894,212772248,12990,SRX3638235,SRS2904486,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.92385,,0.10405,,0.70471,,0.50985,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47602,SRR6661138,SRX3638234,SRS2904485,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidDKOPHZ 2,GSM2975182,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,KidDKOPHZ 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975182,GSM2975182: KidDKOPHZ 2; Danio rerio; RNA Seq,GSM2975182,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975182,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidDKOPHZ_2.fastq.gz,fastq,866844552.0,16996952.0,GSM2975182 r1,0:51,A:235445628;C:198901971;G:200334068;T:232148841;N:14044,51,,,,235445628,198901971,200334068,232148841,14044,SRX3638234,SRS2904485,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.92657,,0.10886,,0.71112,,0.52093,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47603,SRR6661137,SRX3638233,SRS2904484,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidDKOPHZ 1,GSM2975181,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,KidDKOPHZ 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975181,GSM2975181: KidDKOPHZ 1; Danio rerio; RNA Seq,GSM2975181,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975181,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidDKOPHZ_1.fastq.gz,fastq,795526560.0,15598560.0,GSM2975181 r1,0:51,A:216666052;C:181785239;G:183159054;T:213903089;N:13126,51,,,,216666052,181785239,183159054,213903089,13126,SRX3638233,SRS2904484,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.92522,,0.10277,,0.7121,,0.51721,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47604,SRR6661136,SRX3638232,SRS2904483,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidDKO 3,GSM2975180,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,KidDKO 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975180,GSM2975180: KidDKO 3; Danio rerio; RNA Seq,GSM2975180,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975180,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidDKO_3.fastq.gz,fastq,699170577.0,13709227.0,GSM2975180 r1,0:51,A:191094810;C:157413925;G:158857752;T:191792628;N:11462,51,,,,191094810,157413925,158857752,191792628,11462,SRX3638232,SRS2904483,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.9183,,0.12207,,0.7083,,0.52994,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47605,SRR6661135,SRX3638231,SRS2904482,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidDKO 2,GSM2975179,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,KidDKO 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975179,GSM2975179: KidDKO 2; Danio rerio; RNA Seq,GSM2975179,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975179,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidDKO_2.fastq.gz,fastq,720757194.0,14132494.0,GSM2975179 r1,0:51,A:198433339;C:163064446;G:163967236;T:195280391;N:11782,51,,,,198433339,163064446,163967236,195280391,11782,SRX3638231,SRS2904482,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.92921,,0.11261,,0.7063,,0.52644,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 47606,SRR6661134,SRX3638230,SRS2904481,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,KidDKO 1,GSM2975178,,source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,KidDKO 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975178,GSM2975178: KidDKO 1; Danio rerio; RNA Seq,GSM2975178,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975178,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,KidDKO_1.fastq.gz,fastq,835548606.0,16383306.0,GSM2975178 r1,0:51,A:227900020;C:191118125;G:192603640;T:223913065;N:13756,51,,,,227900020,191118125,192603640,223913065,13756,SRX3638230,SRS2904481,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.93166,,0.10926,,0.7063,,0.50705,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Kidney,Renal System 48941,SRR7535399,SRX4403259,SRS3557748,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample43,F3HFL6,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3HFL6 L43,F3HFL6 L43,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3HFL6.fastq.gz,fastq,3513906206.0,41769622.0,F3HFL6.fastq.gz,0:84.13 1:0,A:977114573;C:787720805;G:749651347;T:999364818;N:54663,84,0,,,977114573,787720805,749651347,999364818,54663,SRX4403259,SRS3557748,SRA741696,Gov of Canada,Gov of Canada,1,0.95671,,0.06506,,0.78228,,0.56305,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48942,SRR7535400,SRX4403258,SRS3557747,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample41,F3HFL4,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3HFL4 L41,F3HFL4 L41,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3HFL4.fastq.gz,fastq,1925799513.0,22885356.0,F3HFL4.fastq.gz,0:84.15 1:0,A:524298249;C:430610288;G:398055851;T:572803437;N:31688,84,0,,,524298249,430610288,398055851,572803437,31688,SRX4403258,SRS3557747,SRA741696,Gov of Canada,Gov of Canada,1,0.93737,,0.10113,,0.81022,,0.55692,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48943,SRR7535401,SRX4403257,SRS3557746,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample42,F3HFL5,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3HFL5 L42,F3HFL5 L42,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3HFL5.fastq.gz,fastq,2861742645.0,33977477.0,F3HFL5.fastq.gz,0:84.22 1:0,A:771306767;C:644570838;G:600324085;T:845486554;N:54401,84,0,,,771306767,644570838,600324085,845486554,54401,SRX4403257,SRS3557746,SRA741696,Gov of Canada,Gov of Canada,1,0.95145,,0.08188,,0.78084,,0.53906,,82,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-07-18,Adult,Adult,Kidney,Renal System 48944,SRR7535402,SRX4403256,SRS3557745,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample21,F0HFL8,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0HFL8 L21,F0HFL8 L21,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0HFL8.fastq.gz,fastq,3270195567.0,43558704.0,F0HFL8.fastq.gz,0:75.08 1:0,A:931015183;C:710121529;G:674934313;T:954020799;N:103743,75,0,,,931015183,710121529,674934313,954020799,103743,SRX4403256,SRS3557745,SRA741696,Gov of Canada,Gov of Canada,1,0.94496,,0.07696,,0.74931,,0.55469,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48945,SRR7535403,SRX4403255,SRS3557744,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample22,F3CTR1,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3CTR1 L22,F3CTR1 L22,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3CTR1.fastq.gz,fastq,2224836049.0,29606943.0,F3CTR1.fastq.gz,0:75.15 1:0,A:610515696;C:506550058;G:471139873;T:636560130;N:70292,75,0,,,610515696,506550058,471139873,636560130,70292,SRX4403255,SRS3557744,SRA741696,Gov of Canada,Gov of Canada,1,0.95447,,0.0754,,0.78066,,0.54856,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48946,SRR7535404,SRX4403254,SRS3557743,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample23,F3CTR2,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3CTR2 L23,F3CTR2 L23,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3CTR2.fastq.gz,fastq,3106167820.0,36871227.0,F3CTR2.fastq.gz,0:84.24 1:0,A:844192333;C:713285812;G:657110592;T:891518698;N:60385,84,0,,,844192333,713285812,657110592,891518698,60385,SRX4403254,SRS3557743,SRA741696,Gov of Canada,Gov of Canada,1,0.9554,,0.06997,,0.79275,,0.52557,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48947,SRR7535405,SRX4403253,SRS3557742,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample24,F3CTR3,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3CTR3 L24,F3CTR3 L24,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3CTR3.fastq.gz,fastq,2619378393.0,31091747.0,F3CTR3.fastq.gz,0:84.25 1:0,A:699692748;C:600624113;G:564410765;T:754600796;N:49971,84,0,,,699692748,600624113,564410765,754600796,49971,SRX4403253,SRS3557742,SRA741696,Gov of Canada,Gov of Canada,1,0.95974,,0.06076,,0.7932,,0.54096,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48948,SRR7535406,SRX4403252,SRS3557741,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample25,F3CTR4,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3CTR4 L25,F3CTR4 L25,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3CTR4.fastq.gz,fastq,3292260052.0,39078900.0,F3CTR4.fastq.gz,0:84.25 1:0,A:880017890;C:753064780;G:705989117;T:953125639;N:62626,84,0,,,880017890,753064780,705989117,953125639,62626,SRX4403252,SRS3557741,SRA741696,Gov of Canada,Gov of Canada,1,0.95321,,0.07242,,0.75666,,0.54587,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48949,SRR7535407,SRX4403251,SRS3557740,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample26,F3CTR5,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3CTR5 L26,F3CTR5 L26,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3CTR5.fastq.gz,fastq,3007976354.0,35696121.0,F3CTR5.fastq.gz,0:84.27 1:0,A:778578191;C:708292962;G:650565998;T:870481710;N:57493,84,0,,,778578191,708292962,650565998,870481710,57493,SRX4403251,SRS3557740,SRA741696,Gov of Canada,Gov of Canada,1,0.95344,,0.06722,,0.7597,,0.52143,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48950,SRR7535408,SRX4403250,SRS3557739,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample27,F3CTR6,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3CTR6 L27,F3CTR6 L27,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3CTR6.fastq.gz,fastq,2550867627.0,31161224.0,F3CTR6.fastq.gz,0:81.86 1:0,A:1115959207;C:419324274;G:453781546;T:561761915;N:40685,81,0,,,1115959207,419324274,453781546,561761915,40685,SRX4403250,SRS3557739,SRA741696,Gov of Canada,Gov of Canada,1,0.92888,,0.24434,,0.77749,,0.51629,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48951,SRR7535409,SRX4403249,SRS3557738,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample28,F3CTR7,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3CTR7 L28,F3CTR7 L28,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3CTR7.fastq.gz,fastq,2059768786.0,24468469.0,F3CTR7.fastq.gz,0:84.18 1:0,A:558059300;C:468460643;G:436031484;T:597176496;N:40863,84,0,,,558059300,468460643,436031484,597176496,40863,SRX4403249,SRS3557738,SRA741696,Gov of Canada,Gov of Canada,1,0.94686,,0.07284,,0.77459,,0.54014,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48952,SRR7535410,SRX4403248,SRS3557737,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample29,F3CTR8,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3CTR8 L29,F3CTR8 L29,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3CTR8.fastq.gz,fastq,3053213414.0,36279614.0,F3CTR8.fastq.gz,0:84.16 1:0,A:815581740;C:713814496;G:673475187;T:850294355;N:47636,84,0,,,815581740,713814496,673475187,850294355,47636,SRX4403248,SRS3557737,SRA741696,Gov of Canada,Gov of Canada,1,0.9571,,0.06714,,0.75369,,0.54721,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48953,SRR7535411,SRX4403247,SRS3557736,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample30,F3LFL1,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3LFL1 L30,F3LFL1 L30,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3LFL1.fastq.gz,fastq,2028343411.0,26987895.0,F3LFL1.fastq.gz,0:75.16 1:0,A:548593649;C:466971074;G:433327481;T:579386722;N:64485,75,0,,,548593649,466971074,433327481,579386722,64485,SRX4403247,SRS3557736,SRA741696,Gov of Canada,Gov of Canada,1,0.95498,,0.0741,,0.7895,,0.5309,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-07-18,Adult,Adult,Kidney,Renal System 48954,SRR7535412,SRX4403246,SRS3557735,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample8,F0CTR8,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0CTR8 L8,F0CTR8 L8,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0CTR8.fastq.gz,fastq,2222889019.0,29574868.0,F0CTR8.fastq.gz,0:75.16 1:0,A:596733500;C:518690507;G:486721856;T:620675208;N:67948,75,0,,,596733500,518690507,486721856,620675208,67948,SRX4403246,SRS3557735,SRA741696,Gov of Canada,Gov of Canada,1,0.95446,,0.05545,,0.74815,,0.51889,,74,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48955,SRR7535413,SRX4403245,SRS3557734,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample7,F0CTR7,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0CTR7 L7,F0CTR7 L7,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0CTR7.fastq.gz,fastq,4544318503.0,53947186.0,F0CTR7.fastq.gz,0:84.24 1:0,A:1292030811;C:991354554;G:942494048;T:1318393334;N:45756,84,0,,,1292030811,991354554,942494048,1318393334,45756,SRX4403245,SRS3557734,SRA741696,Gov of Canada,Gov of Canada,1,0.9503,,0.06778,,0.75743,,0.55348,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-07-18,Adult,Adult,Kidney,Renal System 48956,SRR7535414,SRX4403244,SRS3557733,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample6,F0CTR6,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0CTR6 L6,F0CTR6 L6,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0CTR6.fastq.gz,fastq,2358891923.0,31391321.0,F0CTR6.fastq.gz,0:75.14 1:0,A:685288644;C:509459791;G:472389125;T:691678243;N:76120,75,0,,,685288644,509459791,472389125,691678243,76120,SRX4403244,SRS3557733,SRA741696,Gov of Canada,Gov of Canada,1,0.94166,,0.07795,,0.76195,,0.53942,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48957,SRR7535415,SRX4403243,SRS3557732,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample5,F0CTR5,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0CTR5 L5,F0CTR5 L5,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0CTR5.fastq.gz,fastq,2588676344.0,30755117.0,F0CTR5.fastq.gz,0:84.17 1:0,A:720655179;C:582123937;G:551878210;T:733977893;N:41125,84,0,,,720655179,582123937,551878210,733977893,41125,SRX4403243,SRS3557732,SRA741696,Gov of Canada,Gov of Canada,1,0.95586,,0.06561,,0.7808,,0.54698,,83,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48958,SRR7535416,SRX4403242,SRS3557731,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample4,F0CTR4,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0CTR4 L4,F0CTR4 L4,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0CTR4.fastq.gz,fastq,2959885275.0,35175450.0,F0CTR4.fastq.gz,0:84.15 1:0,A:799876836;C:675392846;G:616854860;T:867718008;N:42725,84,0,,,799876836,675392846,616854860,867718008,42725,SRX4403242,SRS3557731,SRA741696,Gov of Canada,Gov of Canada,1,0.93974,,0.07556,,0.76238,,0.50131,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48959,SRR7535417,SRX4403241,SRS3557730,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample3,F0CTR3,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0CTR3 L3,F0CTR3 L3,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0CTR3.fastq.gz,fastq,3127991402.0,37019173.0,F0CTR3.fastq.gz,0:84.50 1:0,A:886233117;C:699410395;G:659031655;T:883271353;N:44882,84,0,,,886233117,699410395,659031655,883271353,44882,SRX4403241,SRS3557730,SRA741696,Gov of Canada,Gov of Canada,1,0.95481,,0.06332,,0.77818,,0.54263,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48960,SRR7535418,SRX4403240,SRS3557729,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample2,F0CTR2,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0CTR2 L2,F0CTR2 L2,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0CTR2.fastq.gz,fastq,4589246236.0,54480219.0,F0CTR2.fastq.gz,0:84.24 1:0,A:1318726005;C:987643623;G:940290206;T:1342543647;N:42755,84,0,,,1318726005,987643623,940290206,1342543647,42755,SRX4403240,SRS3557729,SRA741696,Gov of Canada,Gov of Canada,1,0.94686,,0.06888,,0.76278,,0.55045,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48961,SRR7535419,SRX4403239,SRS3557728,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample1,F0CTR1,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0CTR1 L1,F0CTR1 L1,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0CTR1.fastq.gz,fastq,2895973720.0,34407735.0,F0CTR1.fastq.gz,0:84.17 1:0,A:805217942;C:647195655;G:615425828;T:828086852;N:47443,84,0,,,805217942,647195655,615425828,828086852,47443,SRX4403239,SRS3557728,SRA741696,Gov of Canada,Gov of Canada,1,0.95771,,0.05823,,0.75475,,0.54018,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-07-18,Adult,Adult,Kidney,Renal System 48962,SRR7535420,SRX4403238,SRS3557727,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample10,F0LFL2,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0LFL2 L10,F0LFL2 L10,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0LFL2.fastq.gz,fastq,2221964224.0,29564609.0,F0LFL2.fastq.gz,0:75.16 1:0,A:622205890;C:491850489;G:469917376;T:637922036;N:68433,75,0,,,622205890,491850489,469917376,637922036,68433,SRX4403238,SRS3557727,SRA741696,Gov of Canada,Gov of Canada,1,0.95207,,0.06132,,0.76404,,0.5374,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48963,SRR7535421,SRX4403237,SRS3557726,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample9,F0LFL1,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0LFL1 L9,F0LFL1 L9,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0LFL1.fastq.gz,fastq,3222133895.0,38154313.0,F0LFL1.fastq.gz,0:84.45 1:0,A:920033678;C:715675242;G:671297913;T:915080329;N:46733,84,0,,,920033678,715675242,671297913,915080329,46733,SRX4403237,SRS3557726,SRA741696,Gov of Canada,Gov of Canada,1,0.95496,,0.07355,,0.76644,,0.54508,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48964,SRR7535422,SRX4403236,SRS3557725,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample20,F0HFL7,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0HFL7 L20,F0HFL7 L20,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0HFL7.fastq.gz,fastq,2800528980.0,33270152.0,F0HFL7.fastq.gz,0:84.18 1:0,A:745732773;C:657771159;G:624594638;T:772385369;N:45041,84,0,,,745732773,657771159,624594638,772385369,45041,SRX4403236,SRS3557725,SRA741696,Gov of Canada,Gov of Canada,1,0.9603,,0.05557,,0.75262,,0.53229,,83,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48965,SRR7535423,SRX4403235,SRS3557724,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample19,F0HFL6,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0HFL6 L19,F0HFL6 L19,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0HFL6.fastq.gz,fastq,3859582889.0,45819776.0,F0HFL6.fastq.gz,0:84.23 1:0,A:1042286597;C:895964648;G:843235146;T:1078059877;N:36621,84,0,,,1042286597,895964648,843235146,1078059877,36621,SRX4403235,SRS3557724,SRA741696,Gov of Canada,Gov of Canada,1,0.95288,,0.06929,,0.74,,0.52268,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48966,SRR7535424,SRX4403234,SRS3557723,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample16,F0HFL3,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0HFL3 L16,F0HFL3 L16,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0HFL3.fastq.gz,fastq,3793212903.0,45071794.0,F0HFL3.fastq.gz,0:84.16 1:0,A:1056360853;C:843514256;G:810627279;T:1082649387;N:61128,84,0,,,1056360853,843514256,810627279,1082649387,61128,SRX4403234,SRS3557723,SRA741696,Gov of Canada,Gov of Canada,1,0.95323,,0.06159,,0.76195,,0.54295,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48967,SRR7535425,SRX4403233,SRS3557722,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample15,F0HFL2,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0HFL2 L15,F0HFL2 L15,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0HFL2.fastq.gz,fastq,1653605409.0,19670232.0,F0HFL2.fastq.gz,0:84.07 1:0,A:482659933;C:340033054;G:332925206;T:497960425;N:26791,84,0,,,482659933,340033054,332925206,497960425,26791,SRX4403233,SRS3557722,SRA741696,Gov of Canada,Gov of Canada,1,0.94378,,0.07818,,0.76654,,0.56019,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48968,SRR7535426,SRX4403232,SRS3557721,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample18,F0HFL5,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0HFL5 L18,F0HFL5 L18,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0HFL5.fastq.gz,fastq,2841372173.0,33797215.0,F0HFL5.fastq.gz,0:84.07 1:0,A:778391982;C:632117929;G:585902045;T:844912619;N:47598,84,0,,,778391982,632117929,585902045,844912619,47598,SRX4403232,SRS3557721,SRA741696,Gov of Canada,Gov of Canada,1,0.93559,,0.07561,,0.76895,,0.55817,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48969,SRR7535427,SRX4403231,SRS3557719,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample17,F0HFL4,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0HFL4 L17,F0HFL4 L17,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0HFL4.fastq.gz,fastq,3160174261.0,37565835.0,F0HFL4.fastq.gz,0:84.12 1:0,A:884296991;C:697282059;G:667815635;T:910728716;N:50860,84,0,,,884296991,697282059,667815635,910728716,50860,SRX4403231,SRS3557719,SRA741696,Gov of Canada,Gov of Canada,1,0.95258,,0.06896,,0.75753,,0.53648,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48970,SRR7535428,SRX4403230,SRS3557720,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample12,F0LFL4,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0LFL4 L12,F0LFL4 L12,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0LFL4.fastq.gz,fastq,2872309444.0,34017640.0,F0LFL4.fastq.gz,0:84.44 1:0,A:838123566;C:615148814;G:580099793;T:838897200;N:40071,84,0,,,838123566,615148814,580099793,838897200,40071,SRX4403230,SRS3557720,SRA741696,Gov of Canada,Gov of Canada,1,0.94655,,0.07484,,0.76055,,0.53193,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48971,SRR7535429,SRX4403229,SRS3557718,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample11,F0LFL3,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0LFL3 L11,F0LFL3 L11,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0LFL3.fastq.gz,fastq,4819656374.0,57208863.0,F0LFL3.fastq.gz,0:84.25 1:0,A:1344664833;C:1065935819;G:1021114550;T:1387895714;N:45458,84,0,,,1344664833,1065935819,1021114550,1387895714,45458,SRX4403229,SRS3557718,SRA741696,Gov of Canada,Gov of Canada,1,0.94968,,0.06704,,0.75063,,0.53941,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48972,SRR7535430,SRX4403228,SRS3557717,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample14,F0HFL1,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0HFL1 L14,F0HFL1 L14,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0HFL1.fastq.gz,fastq,4382160649.0,58413517.0,F0HFL1.fastq.gz,0:75.02 1:0,A:1369437301;C:861646512;G:809593345;T:1341341422;N:142069,75,0,,,1369437301,861646512,809593345,1341341422,142069,SRX4403228,SRS3557717,SRA741696,Gov of Canada,Gov of Canada,1,0.9466,,0.08719,,0.7794,,0.54372,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-07-18,Adult,Adult,Kidney,Renal System 48973,SRR7535431,SRX4403227,SRS3557716,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample13,F0LFL5,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F0LFL5 L13,F0LFL5 L13,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F0LFL5.fastq.gz,fastq,4135324561.0,55077889.0,F0LFL5.fastq.gz,0:75.08 1:0,A:1152758595;C:923324532;G:883060803;T:1176048511;N:132120,75,0,,,1152758595,923324532,883060803,1176048511,132120,SRX4403227,SRS3557716,SRA741696,Gov of Canada,Gov of Canada,1,0.94936,,0.07427,,0.7385,,0.54293,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48974,SRR7535432,SRX4403226,SRS3557715,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample38,F3HFL1,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3HFL1 L38,F3HFL1 L38,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3HFL1.fastq.gz,fastq,4205002265.0,49802474.0,F3HFL1.fastq.gz,0:84.43 1:0,A:1296210304;C:849397168;G:835453941;T:1223875076;N:65776,84,0,,,1296210304,849397168,835453941,1223875076,65776,SRX4403226,SRS3557715,SRA741696,Gov of Canada,Gov of Canada,1,0.95559,,0.0917,,0.78044,,0.61361,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48975,SRR7535433,SRX4403225,SRS3557714,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample37,F3LFL8,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3LFL8 L37,F3LFL8 L37,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3LFL8.fastq.gz,fastq,2259705259.0,26829092.0,F3LFL8.fastq.gz,0:84.23 1:0,A:609862793;C:515167321;G:475663194;T:658969872;N:42079,84,0,,,609862793,515167321,475663194,658969872,42079,SRX4403225,SRS3557714,SRA741696,Gov of Canada,Gov of Canada,1,0.94002,,0.10434,,0.75369,,0.51155,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48976,SRR7535434,SRX4403224,SRS3557713,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample36,F3LFL7,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3LFL7 L36,F3LFL7 L36,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3LFL7.fastq.gz,fastq,2341138815.0,27781759.0,F3LFL7.fastq.gz,0:84.27 1:0,A:608466569;C:545924123;G:501493228;T:685210306;N:44589,84,0,,,608466569,545924123,501493228,685210306,44589,SRX4403224,SRS3557713,SRA741696,Gov of Canada,Gov of Canada,1,0.94523,,0.08263,,0.75284,,0.53752,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48977,SRR7535435,SRX4403223,SRS3557712,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample35,F3LFL6,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3LFL6 L35,F3LFL6 L35,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3LFL6.fastq.gz,fastq,2937598885.0,34879736.0,F3LFL6.fastq.gz,0:84.22 1:0,A:782454526;C:678806792;G:617210082;T:859072883;N:54602,84,0,,,782454526,678806792,617210082,859072883,54602,SRX4403223,SRS3557712,SRA741696,Gov of Canada,Gov of Canada,1,0.94207,,0.08495,,0.74897,,0.5069,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48978,SRR7535436,SRX4403222,SRS3557711,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample34,F3LFL5,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3LFL5 L34,F3LFL5 L34,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3LFL5.fastq.gz,fastq,2497066825.0,29658022.0,F3LFL5.fastq.gz,0:84.20 1:0,A:694874960;C:555774576;G:516525097;T:729844057;N:48135,84,0,,,694874960,555774576,516525097,729844057,48135,SRX4403222,SRS3557711,SRA741696,Gov of Canada,Gov of Canada,1,0.94238,,0.09347,,0.76404,,0.51048,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48979,SRR7535437,SRX4403221,SRS3557710,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample33,F3LFL4,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3LFL4 L33,F3LFL4 L33,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3LFL4.fastq.gz,fastq,3167171318.0,37581804.0,F3LFL4.fastq.gz,0:84.27 1:0,A:836474638;C:736638892;G:687417511;T:906580806;N:59471,84,0,,,836474638,736638892,687417511,906580806,59471,SRX4403221,SRS3557710,SRA741696,Gov of Canada,Gov of Canada,1,0.95381,,0.0776,,0.74432,,0.49786,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48980,SRR7535438,SRX4403220,SRS3557709,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample32,F3LFL3,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3LFL3 L32,F3LFL3 L32,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3LFL3.fastq.gz,fastq,3969872568.0,47103172.0,F3LFL3.fastq.gz,0:84.28 1:0,A:1087899347;C:891968649;G:846315646;T:1143611603;N:77323,84,0,,,1087899347,891968649,846315646,1143611603,77323,SRX4403220,SRS3557709,SRA741696,Gov of Canada,Gov of Canada,1,0.94717,,0.08461,,0.74714,,0.53355,,84,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48981,SRR7535439,SRX4403219,SRS3557708,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample31,F3LFL2,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3LFL2 L31,F3LFL2 L31,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3LFL2.fastq.gz,fastq,2401613544.0,31959346.0,F3LFL2.fastq.gz,0:75.15 1:0,A:673230842;C:536445759;G:492980009;T:698882870;N:74064,75,0,,,673230842,536445759,492980009,698882870,74064,SRX4403219,SRS3557708,SRA741696,Gov of Canada,Gov of Canada,1,0.95198,,0.08486,,0.7878,,0.55398,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48982,SRR7535440,SRX4403218,SRS3557706,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample40,F3HFL3,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3HFL3 L40,F3HFL3 L40,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3HFL3.fastq.gz,fastq,2266960447.0,26913177.0,F3HFL3.fastq.gz,0:84.23 1:0,A:590021990;C:520283209;G:479594101;T:677024566;N:36581,84,0,,,590021990,520283209,479594101,677024566,36581,SRX4403218,SRS3557706,SRA741696,Gov of Canada,Gov of Canada,1,0.94897,,0.08251,,0.80848,,0.57355,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 48983,SRR7535441,SRX4403217,SRS3557707,SRP154295,PRJNA481502,Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio,PRJNA481502,Transcriptome Analysis,Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.,,pubmed:30530669,,sample39,F3HFL2,,strain:AB strain|age:6 mpf organism or animal,,,,,,,,,RNA seq of Danio rerio: male kidney,F3HFL2 L39,F3HFL2 L39,mRNA seq from total RNA on Illumina Neoprep,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 500,,SRP154295,,,F3HFL2.fastq.gz,fastq,2749128323.0,32649931.0,F3HFL2.fastq.gz,0:84.20 1:0,A:739282939;C:602311637;G:590565979;T:816929591;N:38177,84,0,,,739282939,602311637,590565979,816929591,38177,SRX4403217,SRS3557707,SRA741696,Gov of Canada,Gov of Canada,1,0.9613,,0.09046,,0.8104,,0.62158,,85,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Canada,2018-12-11,Adult,Adult,Kidney,Renal System 51852,SRR10358701,SRX7068102,SRS5584514,SRP192333,PRJNA532380,Danio rerio SVCV infection,PRJNA532380,Other,Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.,,,,Model organism or animal sample from Danio rerio,miRNA WT SVCV,,strain:Wild type|age:6 month|sex:pooled male and female|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,miRNA WT SVCV,miRNA WT SVCV,miRNA WT SVCV,Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP192333,,,WT-SVCV_1.fastq.gz,fastq,1316699181.0,25817631.0,WT SVCV 1.fastq.gz,0:51,A:276414308;C:338128957;G:380963712;T:321185951;N:6253,51,,,,276414308,338128957,380963712,321185951,6253,SRX7068102,SRS5584514,SRA986546,IIM - CSIC|Biotechnology and Aquaculture,IIM - CSIC,1,0.12679,,0.0134,,0.9931,,0.63608,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Spain,2019-10-29,Adult,Adult,Kidney,Renal System 51853,SRR10358540,SRX7067941,SRS5584353,SRP192333,PRJNA532380,Danio rerio SVCV infection,PRJNA532380,Other,Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.,,,,Model organism or animal sample from Danio rerio,miRNA WT Control,,strain:Wild type|age:6 month|sex:pooled male and female|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,miRNA WT Control,miRNA WT Control,miRNA WT Control,Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP192333,,,WT-C_1.fastq.gz,fastq,1391330184.0,27280984.0,WT C 1.fastq.gz,0:51,A:252097427;C:365291036;G:426841004;T:347094254;N:6463,51,,,,252097427,365291036,426841004,347094254,6463,SRX7067941,SRS5584353,SRA986495,IIM - CSIC|Biotechnology and Aquaculture,IIM - CSIC,1,0.01783,,0.00242,,0.99411,,0.61368,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Spain,2019-10-29,Adult,Adult,Kidney,Renal System 60502,SRR12338629,SRX8838545,SRS7101853,SRP273930,PRJNA649208,A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation,GSE155258,Transcriptome Analysis,Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 75 basepair bp single reads SR75 to a depth of approximately 20 million reads per sample on an Illumina HiSeq 4000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software Illumina San Diego CA.,,,,AMut3 S16,GSM4698247,,source name:grna / mutant fish|tissue:kidney marrow|genotype:grna / ,AMut3 S16,RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.,grna / mutant fish,Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.,tissue:kidney marrow|genotype:grna / ,GSM4698247,GSM4698247: AMut3 S16; Danio rerio; RNA Seq,GSM4698247,,1,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,GEO Accession:GSM4698247,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP273930,,,AMut3_S16_L003_R1_001.fastq.gz,fastq,1660975744.0,21854944.0,GSM4698247 r1,0:76 1:0,A:403133854;C:408666497;G:390547168;T:458402036;N:226189,76,0,,,403133854,408666497,390547168,458402036,226189,SRX8838545,SRS7101853,SRA1104643,GEO,"Boolean, Pediatrics, UCSD",1,0.88856,,0.071,,0.7331,,0.50274,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-07-28,Undetermined,Undetermined,Kidney,Renal System 60503,SRR12338628,SRX8838544,SRS7101852,SRP273930,PRJNA649208,A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation,GSE155258,Transcriptome Analysis,Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 75 basepair bp single reads SR75 to a depth of approximately 20 million reads per sample on an Illumina HiSeq 4000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software Illumina San Diego CA.,,,,AMut2 S15,GSM4698246,,source name:grna / mutant fish|tissue:kidney marrow|genotype:grna / ,AMut2 S15,RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.,grna / mutant fish,Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.,tissue:kidney marrow|genotype:grna / ,GSM4698246,GSM4698246: AMut2 S15; Danio rerio; RNA Seq,GSM4698246,,1,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,GEO Accession:GSM4698246,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP273930,,,AMut2_S15_L003_R1_001.fastq.gz,fastq,1932204620.0,25423745.0,GSM4698246 r1,0:76 1:0,A:471753150;C:472824626;G:455434892;T:531926834;N:265118,76,0,,,471753150,472824626,455434892,531926834,265118,SRX8838544,SRS7101852,SRA1104643,GEO,"Boolean, Pediatrics, UCSD",1,0.88563,,0.0647,,0.73054,,0.51301,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-07-28,Undetermined,Undetermined,Kidney,Renal System 60504,SRR12338627,SRX8838543,SRS7101851,SRP273930,PRJNA649208,A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation,GSE155258,Transcriptome Analysis,Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 75 basepair bp single reads SR75 to a depth of approximately 20 million reads per sample on an Illumina HiSeq 4000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software Illumina San Diego CA.,,,,AMut1 S14,GSM4698245,,source name:grna / mutant fish|tissue:kidney marrow|genotype:grna / ,AMut1 S14,RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.,grna / mutant fish,Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.,tissue:kidney marrow|genotype:grna / ,GSM4698245,GSM4698245: AMut1 S14; Danio rerio; RNA Seq,GSM4698245,,1,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,GEO Accession:GSM4698245,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP273930,,,AMut1_S14_L003_R1_001.fastq.gz,fastq,1576218644.0,20739719.0,GSM4698245 r1,0:76 1:0,A:382135276;C:389342906;G:367829537;T:436699819;N:211106,76,0,,,382135276,389342906,367829537,436699819,211106,SRX8838543,SRS7101851,SRA1104643,GEO,"Boolean, Pediatrics, UCSD",1,0.88823,,0.07406,,0.73062,,0.50537,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-07-28,Undetermined,Undetermined,Kidney,Renal System 60505,SRR12338626,SRX8838542,SRS7101850,SRP273930,PRJNA649208,A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation,GSE155258,Transcriptome Analysis,Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 75 basepair bp single reads SR75 to a depth of approximately 20 million reads per sample on an Illumina HiSeq 4000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software Illumina San Diego CA.,,,,WT3 S13,GSM4698244,,source name:grna+/+ control fish|tissue:kidney marrow|genotype:WT,WT3 S13,RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.,grna+/+ control fish,Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.,tissue:kidney marrow|genotype:WT,GSM4698244,GSM4698244: WT3 S13; Danio rerio; RNA Seq,GSM4698244,,1,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,GEO Accession:GSM4698244,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP273930,,,WT3_S13_L003_R1_001.fastq.gz,fastq,1763410824.0,23202774.0,GSM4698244 r1,0:76 1:0,A:423301555;C:439721210;G:408339976;T:491805474;N:242609,76,0,,,423301555,439721210,408339976,491805474,242609,SRX8838542,SRS7101850,SRA1104643,GEO,"Boolean, Pediatrics, UCSD",1,0.89892,,0.06886,,0.74408,,0.49795,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-07-28,Undetermined,Undetermined,Kidney,Renal System 60506,SRR12338625,SRX8838541,SRS7101849,SRP273930,PRJNA649208,A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation,GSE155258,Transcriptome Analysis,Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 75 basepair bp single reads SR75 to a depth of approximately 20 million reads per sample on an Illumina HiSeq 4000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software Illumina San Diego CA.,,,,WT2 S12,GSM4698243,,source name:grna+/+ control fish|tissue:kidney marrow|genotype:WT,WT2 S12,RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.,grna+/+ control fish,Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.,tissue:kidney marrow|genotype:WT,GSM4698243,GSM4698243: WT2 S12; Danio rerio; RNA Seq,GSM4698243,,1,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,GEO Accession:GSM4698243,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP273930,,,WT2_S12_L003_R1_001.fastq.gz,fastq,1637691700.0,21548575.0,GSM4698243 r1,0:76 1:0,A:405974612;C:400305204;G:377359541;T:453830617;N:221726,76,0,,,405974612,400305204,377359541,453830617,221726,SRX8838541,SRS7101849,SRA1104643,GEO,"Boolean, Pediatrics, UCSD",1,0.89995,,0.07959,,0.7429,,0.5021,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-07-28,Undetermined,Undetermined,Kidney,Renal System 60507,SRR12338624,SRX8838540,SRS7101848,SRP273930,PRJNA649208,A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation,GSE155258,Transcriptome Analysis,Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 75 basepair bp single reads SR75 to a depth of approximately 20 million reads per sample on an Illumina HiSeq 4000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software Illumina San Diego CA.,,,,WT1 S11,GSM4698242,,source name:grna+/+ control fish|tissue:kidney marrow|genotype:WT,WT1 S11,RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample.,grna+/+ control fish,Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines.,tissue:kidney marrow|genotype:WT,GSM4698242,GSM4698242: WT1 S11; Danio rerio; RNA Seq,GSM4698242,,1,Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes.,GEO Accession:GSM4698242,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP273930,,,WT1_S11_L003_R1_001.fastq.gz,fastq,1817974948.0,23920723.0,GSM4698242 r1,0:76 1:0,A:445440119;C:445993982;G:423050638;T:503235344;N:254865,76,0,,,445440119,445993982,423050638,503235344,254865,SRX8838540,SRS7101848,SRA1104643,GEO,"Boolean, Pediatrics, UCSD",1,0.89811,,0.07554,,0.72908,,0.4892,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2020-07-28,Undetermined,Undetermined,Kidney,Renal System 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,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,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,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 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,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,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,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,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,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,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,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,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