{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", tissue_curation = \"Kidney\" and tissue_curation_coarse = \"Renal System\"", "rows": [[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.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 F K", null, "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", null, null, null, null, null, null, null, null, "Iso Seq RNA from kidney", "C2 F2 F K", "C2 F2 F K", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "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, null, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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. 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This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 M K22", null, "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", null, null, null, null, null, null, null, null, "Iso Seq RNA from kidney", "C2 F2 M K22", "C2 F2 M K22", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "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, null, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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. 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This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 M K21", null, "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", null, null, null, null, null, null, null, null, "Iso Seq RNA from kidney", "C2 F2 M K21", "C2 F2 M K21", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "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, null, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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 \u00b5L 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.", null, "pubmed:25535281", null, "24K", "GSM1541905", null, "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", null, "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", null, "tissue:head kidney|disease state:24h post SVCV infection", "GSM1541905", "GSM1541905: 24K; Danio rerio; RNA Seq", "GSM1541905", null, "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", null, "SRP049663", null, null, "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, null, null, null, 266117014, 246797067, 240014464, 267491299, 67716, "SRX756916", "SRS742120", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.92411, null, 0.07686, null, 0.68647, null, 0.4627, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "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 \u00b5L 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.", null, "pubmed:25535281", null, "6K", "GSM1541904", null, "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", null, "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", null, "tissue:head kidney|disease state:6h post SVCV infection", "GSM1541904", "GSM1541904: 6K; Danio rerio; RNA Seq", "GSM1541904", null, "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", null, "SRP049663", null, null, "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, null, null, null, 242005719, 225485975, 219890494, 241993975, 59873, "SRX756915", "SRS742117", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.92547, null, 0.09105, null, 0.69264, null, 0.49166, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "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 \u00b5L 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.", null, "pubmed:25535281", null, "0K", "GSM1541903", null, "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", null, "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", null, "tissue:head kidney|disease state:un infected", "GSM1541903", "GSM1541903: 0K; Danio rerio; RNA Seq", "GSM1541903", null, "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", null, "SRP049663", null, null, "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, null, null, null, 280277150, 261348733, 255721013, 280562071, 70128, "SRX756914", "SRS742116", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.92545, null, 0.08181, null, 0.68373, null, 0.49408, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Kidney", "Renal System"], [41902, "SRR5337748", "SRX2635098", "SRS2043910", "SRP101756", "PRJNA378882", "Transcriptome of the distal late segment of the zebrafish mesonephros", "GSE96519", "Transcriptome Analysis", "We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.", null, "pubmed:28656378", null, "YS6", "GSM2534771", null, "tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult", "YS6", "none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts", "Mesonephros DL", null, "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", null, "transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult", "GSM2534771", "GSM2534771: YS6; Danio rerio; RNA Seq", "GSM2534771", null, "1", "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", "GEO Accession:GSM2534771", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101756", null, null, "20150717.A-YS6_R1.fastq.gz", "fastq", 5434051896.0, 43127396.0, "GSM2534771 r1", "0:126", "A:1185876928;C:1354521221;G:1643633065;T:1249907593;N:113089", 126, null, null, null, 1185876928, 1354521221, 1643633065, 1249907593, 113089, "SRX2635098", "SRS2043910", "SRA544882", "GEO", "Drummond, Nephrology, Massachusetts General Hospital", 1, 0.97351, null, 0.17501, null, 0.85303, null, 0.75625, null, 126, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2017-03-12", "Adult", "Adult", "Kidney", "Renal System"], [41903, "SRR5337747", "SRX2635097", "SRS2043909", "SRP101756", "PRJNA378882", "Transcriptome of the distal late segment of the zebrafish mesonephros", "GSE96519", "Transcriptome Analysis", "We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.", null, "pubmed:28656378", null, "YS5", "GSM2534770", null, "tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult", "YS5", "none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts", "DL segments", null, "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", null, "transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult", "GSM2534770", "GSM2534770: YS5; Danio rerio; RNA Seq", "GSM2534770", null, "1", "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", "GEO Accession:GSM2534770", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101756", null, null, "20150717.A-YS5_R1.fastq(1).gz", "fastq", 2297696058.0, 18235683.0, "GSM2534770 r1", "0:126", "A:648837532;C:505738661;G:568578688;T:574489076;N:52101", 126, null, null, null, 648837532, 505738661, 568578688, 574489076, 52101, "SRX2635097", "SRS2043909", "SRA544882", "GEO", "Drummond, Nephrology, Massachusetts General Hospital", 1, 0.94402, null, 0.1927, null, 0.77585, null, 0.67728, null, 126, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2017-03-12", "Adult", "Adult", "Kidney", "Renal System"], [41904, "SRR5337746", "SRX2635096", "SRS2043908", "SRP101756", "PRJNA378882", "Transcriptome of the distal late segment of the zebrafish mesonephros", "GSE96519", "Transcriptome Analysis", "We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.", null, "pubmed:28656378", null, "YS4", "GSM2534769", null, "tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult", "YS4", "none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts", "Mesonephros DL", null, "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", null, "transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult", "GSM2534769", "GSM2534769: YS4; Danio rerio; RNA Seq", "GSM2534769", null, "1", "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. 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To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.", null, "pubmed:28656378", null, "YS3", "GSM2534768", null, "tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult", "YS3", "none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts", "DL segments", null, "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", null, "transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult", "GSM2534768", "GSM2534768: YS3; Danio rerio; RNA Seq", "GSM2534768", null, "1", "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", "GEO Accession:GSM2534768", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101756", null, null, "20150717.A-YS3_R1.fastq.gz", "fastq", 5648398686.0, 44828561.0, "GSM2534768 r1", "0:126", "A:1607436982;C:1222995706;G:1369036558;T:1448805498;N:123942", 126, null, null, null, 1607436982, 1222995706, 1369036558, 1448805498, 123942, "SRX2635095", "SRS2043907", "SRA544882", "GEO", "Drummond, Nephrology, Massachusetts General Hospital", 1, 0.93399, null, 0.20266, null, 0.78076, null, 0.73978, null, 126, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2017-03-12", "Adult", "Adult", "Kidney", "Renal System"], [41906, "SRR5337744", "SRX2635094", "SRS2043906", "SRP101756", "PRJNA378882", "Transcriptome of the distal late segment of the zebrafish mesonephros", "GSE96519", "Transcriptome Analysis", "We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.", null, "pubmed:28656378", null, "YS2", "GSM2534767", null, "tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult", "YS2", "none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts", "Mesonephros DL", null, "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", null, "transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult", "GSM2534767", "GSM2534767: YS2; Danio rerio; RNA Seq", "GSM2534767", null, "1", "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", "GEO Accession:GSM2534767", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101756", null, null, "20150717.A-YS2_R1.fastq.gz", "fastq", 4680679374.0, 37148249.0, "GSM2534767 r1", "0:126", "A:1320151433;C:986429614;G:1112497899;T:1261495719;N:104709", 126, null, null, null, 1320151433, 986429614, 1112497899, 1261495719, 104709, "SRX2635094", "SRS2043906", "SRA544882", "GEO", "Drummond, Nephrology, Massachusetts General Hospital", 1, 0.91952, null, 0.24724, null, 0.73884, null, 0.63985, null, 126, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2017-03-12", "Adult", "Adult", "Kidney", "Renal System"], [41907, "SRR5337743", "SRX2635093", "SRS2043905", "SRP101756", "PRJNA378882", "Transcriptome of the distal late segment of the zebrafish mesonephros", "GSE96519", "Transcriptome Analysis", "We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.", null, "pubmed:28656378", null, "YS1", "GSM2534766", null, "tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult", "YS1", "none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts", "DL segments", null, "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", null, "transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult", "GSM2534766", "GSM2534766: YS1; Danio rerio; RNA Seq", "GSM2534766", null, "1", "DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", "GEO Accession:GSM2534766", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101756", null, null, "20150717.A-YS1_R1.fastq.gz", "fastq", 7000703892.0, 55561142.0, "GSM2534766 r1", "0:126", "A:1521231890;C:1760818628;G:2148863730;T:1569634203;N:155441", 126, null, null, null, 1521231890, 1760818628, 2148863730, 1569634203, 155441, "SRX2635093", "SRS2043905", "SRA544882", "GEO", "Drummond, Nephrology, Massachusetts General Hospital", 1, 0.96016, null, 0.1982, null, 0.86261, null, 0.75572, null, 126, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2017-03-12", "Adult", "Adult", "Kidney", "Renal System"], [42599, "SRR5810682", "SRX2989237", "SRS2341160", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 2", "GSM2696104", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696104", "GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq", "GSM2696104", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run2_R1.fastq.gz", "fastq", 23315853588.0, 382227108.0, "GSM2696104 r1", "0:61 1:0", "A:6573828142;C:5137891481;G:5021324431;T:6582457296;N:352238", 61, 0, null, null, 6573828142, 5137891481, 5021324431, 6582457296, 352238, "SRX2989237", "SRS2341160", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.83828, null, 0.08537, null, 0.83552, null, 0.56658, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42600, "SRR5810683", "SRX2989237", "SRS2341160", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 2", "GSM2696104", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696104", "GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq", "GSM2696104", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run2_R2.fastq.gz", "fastq", 3057816864.0, 382227108.0, "GSM2696104 r2", "0:0 1:8", "A:743619897;C:720488231;G:1031094190;T:562297818;N:316728", 0, 8, null, null, 743619897, 720488231, 1031094190, 562297818, 316728, "SRX2989237", "SRS2341160", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42601, "SRR5810684", "SRX2989237", "SRS2341160", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 2", "GSM2696104", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696104", "GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq", "GSM2696104", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run2_R3.fastq.gz", "fastq", 3057816864.0, 382227108.0, "GSM2696104 r3", "0:8", "A:913664473;C:577895371;G:646194239;T:918893384;N:1169397", 8, null, null, null, 913664473, 577895371, 646194239, 918893384, 1169397, "SRX2989237", "SRS2341160", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42602, "SRR5810685", "SRX2989237", "SRS2341160", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 2", "GSM2696104", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696104", "GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq", "GSM2696104", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run2_R4.fastq.gz", "fastq", 5351179512.0, 382227108.0, "GSM2696104 r4", "0:14", "A:1351470715;C:1294400719;G:1379073889;T:1322397488;N:3836701", 14, null, null, null, 1351470715, 1294400719, 1379073889, 1322397488, 3836701, "SRX2989237", "SRS2341160", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 14, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42603, "SRR5810678", "SRX2989236", "SRS2341159", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 1", "GSM2696103", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696103", "GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq", "GSM2696103", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run1_R1.fastq.gz", "fastq", 26868371039.0, 440465099.0, "GSM2696103 r1", "0:61 1:0", "A:7598044404;C:5948542485;G:5746339343;T:7575168754;N:276053", 61, 0, null, null, 7598044404, 5948542485, 5746339343, 7575168754, 276053, "SRX2989236", "SRS2341159", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.83437, null, 0.08222, null, 0.82658, null, 0.54569, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42604, "SRR5810679", "SRX2989236", "SRS2341159", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 1", "GSM2696103", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696103", "GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq", "GSM2696103", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run1_R2.fastq.gz", "fastq", 3523720792.0, 440465099.0, "GSM2696103 r2", "0:0 1:8", "A:892841722;C:781074758;G:1176856476;T:672376743;N:571093", 0, 8, null, null, 892841722, 781074758, 1176856476, 672376743, 571093, "SRX2989236", "SRS2341159", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42605, "SRR5810680", "SRX2989236", "SRS2341159", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 1", "GSM2696103", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696103", "GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq", "GSM2696103", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run1_R3.fastq.gz", "fastq", 3523720792.0, 440465099.0, "GSM2696103 r3", "0:8", "A:1016854893;C:682256486;G:759860179;T:1063129659;N:1619575", 8, null, null, null, 1016854893, 682256486, 759860179, 1063129659, 1619575, "SRX2989236", "SRS2341159", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42606, "SRR5810681", "SRX2989236", "SRS2341159", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of multiple samples 1", "GSM2696103", null, "source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "inDrop sequencing of multiple samples 1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes", "GSM2696103", "GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq", "GSM2696103", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "inDrop_v3_run1_R4.fastq.gz", "fastq", 6166511386.0, 440465099.0, "GSM2696103 r4", "0:14", "A:1513770161;C:1469643118;G:1669791951;T:1509862301;N:3443855", 14, null, null, null, 1513770161, 1469643118, 1669791951, 1509862301, 3443855, "SRX2989236", "SRS2341159", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 14, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42607, "SRR5810676", "SRX2989235", "SRS2341158", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2", "GSM2696102", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "GSM2696102", "GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq", "GSM2696102", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "PRKDC2_R1.fastq.gz", "fastq", 1987929396.0, 55220261.0, "GSM2696102 r1", "0:36 1:0", "A:506372087;C:413396954;G:415448050;T:652683387;N:28918", 36, 0, null, null, 506372087, 413396954, 415448050, 652683387, 28918, "SRX2989235", "SRS2341158", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.86587, null, 0.12447, null, 0.80336, null, 0.54126, null, 36, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42608, "SRR5810677", "SRX2989235", "SRS2341158", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2", "GSM2696102", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "GSM2696102", "GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq", "GSM2696102", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "PRKDC2_R2.fastq.gz", "fastq", 2761013050.0, 55220261.0, "GSM2696102 r2", "0:0 1:50", "A:554483675;C:506568509;G:721419849;T:974751566;N:3789451", 0, 50, null, null, 554483675, 506568509, 721419849, 974751566, 3789451, "SRX2989235", "SRS2341158", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.00796, null, 0.0077, null, 0.99961, null, 0.78947, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42609, "SRR5810674", "SRX2989234", "SRS2341157", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1", "GSM2696101", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "GSM2696101", "GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq", "GSM2696101", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696101", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "PRKDC1_R1.fastq.gz", "fastq", 1549442736.0, 43040076.0, "GSM2696101 r1", "0:36 1:0", "A:402261661;C:326108405;G:319637981;T:501413963;N:20726", 36, 0, null, null, 402261661, 326108405, 319637981, 501413963, 20726, "SRX2989234", "SRS2341157", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.84263, null, 0.11449, null, 0.79464, null, 0.57001, null, 36, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42610, "SRR5810675", "SRX2989234", "SRS2341157", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1", "GSM2696101", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs", "GSM2696101", "GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq", "GSM2696101", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696101", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "PRKDC1_R2.fastq.gz", "fastq", 2152003800.0, 43040076.0, "GSM2696101 r2", "0:0 1:50", "A:432547886;C:403759182;G:561234660;T:751564536;N:2897536", 0, 50, null, null, 432547886, 403759182, 561234660, 751564536, 2897536, "SRX2989234", "SRS2341157", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.00796, null, 0.00773, null, 0.99971, null, 0.82758, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42611, "SRR5810672", "SRX2989233", "SRS2341156", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of WT sample animal #2", "GSM2696100", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "inDrop sequencing of WT sample animal #2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "GSM2696100", "GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq", "GSM2696100", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "WT2_R1.fastq.gz", "fastq", 3202042500.0, 88945625.0, "GSM2696100 r1", "0:36 1:0", "A:821476951;C:657776656;G:665293293;T:1057448635;N:46965", 36, 0, null, null, 821476951, 657776656, 665293293, 1057448635, 46965, "SRX2989233", "SRS2341156", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.84222, null, 0.12969, null, 0.80683, null, 0.53542, null, 36, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42612, "SRR5810673", "SRX2989233", "SRS2341156", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of WT sample animal #2", "GSM2696100", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "inDrop sequencing of WT sample animal #2", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "GSM2696100", "GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq", "GSM2696100", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "WT2_R2.fastq.gz", "fastq", 4447281250.0, 88945625.0, "GSM2696100 r2", "0:0 1:50", "A:880464480;C:827380868;G:1171423978;T:1561925150;N:6086774", 0, 50, null, null, 880464480, 827380868, 1171423978, 1561925150, 6086774, "SRX2989233", "SRS2341156", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.00782, null, 0.0075, null, 0.99947, null, 0.91666, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42613, "SRR5810670", "SRX2989232", "SRS2341155", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of WT sample animal #1", "GSM2696099", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "inDrop sequencing of WT sample animal #1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "GSM2696099", "GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq", "GSM2696099", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "WT1_R1.fastq.gz", "fastq", 3313205496.0, 92033486.0, "GSM2696099 r1", "0:36 1:0", "A:858288917;C:693848400;G:675650809;T:1085369048;N:48322", 36, 0, null, null, 858288917, 693848400, 675650809, 1085369048, 48322, "SRX2989232", "SRS2341155", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.8771, null, 0.13918, null, 0.81115, null, 0.59004, null, 36, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42614, "SRR5810671", "SRX2989232", "SRS2341155", "SRP111339", "PRJNA393429", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops]", "GSE100910", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "inDrop sequencing of WT sample animal #1", "GSM2696099", null, "source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "inDrop sequencing of WT sample animal #1", "Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file \"inDrop GEO supplementary.xlsx \" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.", "Whole kidney marrow", null, "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", null, "indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype", "GSM2696099", "GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq", "GSM2696099", null, "1", "RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.", "GEO Accession:GSM2696099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP111339", null, null, "WT1_R2.fastq.gz", "fastq", 4601674300.0, 92033486.0, "GSM2696099 r2", "0:0 1:50", "A:914884703;C:856837987;G:1192418010;T:1631240786;N:6292814", 0, 50, null, null, 914884703, 856837987, 1192418010, 1631240786, 6292814, "SRX2989232", "SRS2341155", "SRA584587", "GEO", "Pathology, Massachusetts General Hospital", 1, 0.0063, null, 0.00598, null, 0.99959, null, 0.8913, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2017-07-07", "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidWTPHZ 3", "GSM2975189", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidWTPHZ_3.fastq.gz", "fastq", 858099990.0, 16825490.0, "GSM2975189 r1", "0:51", "A:231903062;C:197865548;G:200825484;T:227491985;N:13911", 51, null, null, null, 231903062, 197865548, 200825484, 227491985, 13911, "SRX3638241", "SRS2904492", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.9605, null, 0.10316, null, 0.70721, null, 0.51089, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidWTPHZ 2", "GSM2975188", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidWTPHZ_2.fastq.gz", "fastq", 799571013.0, 15677863.0, "GSM2975188 r1", "0:51", "A:217401512;C:183178629;G:185275617;T:213702318;N:12937", 51, null, null, null, 217401512, 183178629, 185275617, 213702318, 12937, "SRX3638240", "SRS2904491", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.96209, null, 0.10882, null, 0.70861, null, 0.5149, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidWTPHZ 1", "GSM2975187", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidWTPHZ_1.fastq.gz", "fastq", 816038505.0, 16000755.0, "GSM2975187 r1", "0:51", "A:218420574;C:190260181;G:192288409;T:215056318;N:13023", 51, null, null, null, 218420574, 190260181, 192288409, 215056318, 13023, "SRX3638239", "SRS2904490", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.96264, null, 0.09527, null, 0.70834, null, 0.51477, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidWT 3", "GSM2975186", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidWT_3.fastq.gz", "fastq", 852094026.0, 16707726.0, "GSM2975186 r1", "0:51", "A:234167802;C:192807979;G:194651214;T:230453461;N:13570", 51, null, null, null, 234167802, 192807979, 194651214, 230453461, 13570, "SRX3638238", "SRS2904489", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.95788, null, 0.12336, null, 0.70258, null, 0.48964, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidWT 2", "GSM2975185", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidWT_2.fastq.gz", "fastq", 969772038.0, 19015138.0, "GSM2975185 r1", "0:51", "A:265582126;C:219526888;G:222468938;T:262178447;N:15639", 51, null, null, null, 265582126, 219526888, 222468938, 262178447, 15639, "SRX3638237", "SRS2904488", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.95803, null, 0.12522, null, 0.69794, null, 0.50805, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidWT 1", "GSM2975184", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidWT_1.fastq.gz", "fastq", 815590011.0, 15991961.0, "GSM2975184 r1", "0:51", "A:224190865;C:184406547;G:186159880;T:220819162;N:13557", 51, null, null, null, 224190865, 184406547, 186159880, 220819162, 13557, "SRX3638236", "SRS2904487", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.95883, null, 0.13181, null, 0.7023, null, 0.49523, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidDKOPHZ 3", "GSM2975183", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidDKOPHZ_3.fastq.gz", "fastq", 789588885.0, 15482135.0, "GSM2975183 r1", "0:51", "A:215354577;C:180286176;G:181162894;T:212772248;N:12990", 51, null, null, null, 215354577, 180286176, 181162894, 212772248, 12990, "SRX3638235", "SRS2904486", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.92385, null, 0.10405, null, 0.70471, null, 0.50985, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidDKOPHZ 2", "GSM2975182", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidDKOPHZ_2.fastq.gz", "fastq", 866844552.0, 16996952.0, "GSM2975182 r1", "0:51", "A:235445628;C:198901971;G:200334068;T:232148841;N:14044", 51, null, null, null, 235445628, 198901971, 200334068, 232148841, 14044, "SRX3638234", "SRS2904485", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.92657, null, 0.10886, null, 0.71112, null, 0.52093, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidDKOPHZ 1", "GSM2975181", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidDKOPHZ_1.fastq.gz", "fastq", 795526560.0, 15598560.0, "GSM2975181 r1", "0:51", "A:216666052;C:181785239;G:183159054;T:213903089;N:13126", 51, null, null, null, 216666052, 181785239, 183159054, 213903089, 13126, "SRX3638233", "SRS2904484", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.92522, null, 0.10277, null, 0.7121, null, 0.51721, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidDKO 3", "GSM2975180", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidDKO_3.fastq.gz", "fastq", 699170577.0, 13709227.0, "GSM2975180 r1", "0:51", "A:191094810;C:157413925;G:158857752;T:191792628;N:11462", 51, null, null, null, 191094810, 157413925, 158857752, 191792628, 11462, "SRX3638232", "SRS2904483", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.9183, null, 0.12207, null, 0.7083, null, 0.52994, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidDKO 2", "GSM2975179", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidDKO_2.fastq.gz", "fastq", 720757194.0, 14132494.0, "GSM2975179 r1", "0:51", "A:198433339;C:163064446;G:163967236;T:195280391;N:11782", 51, null, null, null, 198433339, 163064446, 163967236, 195280391, 11782, "SRX3638231", "SRS2904482", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.92921, null, 0.11261, null, 0.7063, null, 0.52644, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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 T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc 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.", null, "pubmed:30248094", null, "KidDKO 1", "GSM2975178", null, "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 \u00b5g/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", null, "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", null, "SRP131956", null, null, "KidDKO_1.fastq.gz", "fastq", 835548606.0, 16383306.0, "GSM2975178 r1", "0:51", "A:227900020;C:191118125;G:192603640;T:223913065;N:13756", 51, null, null, null, 227900020, 191118125, 192603640, 223913065, 13756, "SRX3638230", "SRS2904481", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.93166, null, 0.10926, null, 0.7063, null, 0.50705, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:30530669", null, "sample43", "F3HFL6", null, "strain:AB strain|age:6 mpf organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: male kidney", "F3HFL6 L43", "F3HFL6 L43", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "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, null, null, 977114573, 787720805, 749651347, 999364818, 54663, "SRX4403259", "SRS3557748", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95671, null, 0.06506, null, 0.78228, null, 0.56305, null, 84, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:30530669", null, "sample41", "F3HFL4", null, "strain:AB strain|age:6 mpf organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: male kidney", "F3HFL4 L41", "F3HFL4 L41", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "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, null, null, 524298249, 430610288, 398055851, 572803437, 31688, "SRX4403258", "SRS3557747", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.93737, null, 0.10113, null, 0.81022, null, 0.55692, null, 84, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:30530669", null, "sample42", "F3HFL5", null, "strain:AB strain|age:6 mpf organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: male kidney", "F3HFL5 L42", "F3HFL5 L42", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "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, null, null, 771306767, 644570838, 600324085, 845486554, 54401, "SRX4403257", "SRS3557746", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95145, null, 0.08188, null, 0.78084, null, 0.53906, null, 82, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:30530669", null, "sample21", "F0HFL8", null, "strain:AB strain|age:6 mpf organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: male kidney", "F0HFL8 L21", "F0HFL8 L21", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "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, null, null, 931015183, 710121529, 674934313, 954020799, 103743, "SRX4403256", "SRS3557745", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94496, null, 0.07696, null, 0.74931, null, 0.55469, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:30530669", null, "sample22", "F3CTR1", null, "strain:AB strain|age:6 mpf organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: male kidney", "F3CTR1 L22", "F3CTR1 L22", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3CTR1.fastq.gz", "fastq", 2224836049.0, 29606943.0, 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dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", null, "pubmed:31158233", null, "G2 pod 03", "GSM3317057", null, "tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G2 mRNA", "G2 pod 03", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish podocyte", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:pod:mCherry|treatment:human APOL1 G2 mRNA", "GSM3317057", "GSM3317057: G2 pod 03; Danio rerio; RNA Seq", "GSM3317057", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317057", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S9_trimmed.fastq.gz", "fastq", 1265733350.0, 25073196.0, "GSM3317057 r1", "0:50.48 1:0", "A:351449147;C:285891495;G:278677300;T:349486454;N:228954", 50, 0, null, null, 351449147, 285891495, 278677300, 349486454, 228954, "SRX4497216", "SRS3618216", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.88664, null, 0.09978, null, 0.70747, null, 0.46307, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Kidney", "Renal System"], [49050, "SRR7633484", "SRX4497215", "SRS3618215", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", null, "pubmed:31158233", null, "G2 pod 02", "GSM3317056", null, "tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G2 mRNA", "G2 pod 02", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish podocyte", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:pod:mCherry|treatment:human APOL1 G2 mRNA", "GSM3317056", "GSM3317056: G2 pod 02; Danio rerio; RNA Seq", "GSM3317056", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317056", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S8_trimmed.fastq.gz", "fastq", 927703036.0, 18397661.0, "GSM3317056 r1", "0:50.43 1:0", "A:256098583;C:212027468;G:205646180;T:253765375;N:165430", 50, 0, null, null, 256098583, 212027468, 205646180, 253765375, 165430, "SRX4497215", "SRS3618215", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.82269, null, 0.09332, null, 0.70676, null, 0.47673, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Kidney", "Renal System"], [49051, "SRR7633483", "SRX4497214", "SRS3618214", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", null, "pubmed:31158233", null, "G2 pod 01", "GSM3317055", null, "tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G2 mRNA", "G2 pod 01", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish podocyte", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:pod:mCherry|treatment:human APOL1 G2 mRNA", "GSM3317055", "GSM3317055: G2 pod 01; Danio rerio; RNA Seq", "GSM3317055", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317055", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S7_trimmed.fastq.gz", "fastq", 1868917850.0, 36965227.0, "GSM3317055 r1", "0:50.56 1:0", "A:518334465;C:423085551;G:412301170;T:514857394;N:339270", 50, 0, null, null, 518334465, 423085551, 412301170, 514857394, 339270, "SRX4497214", "SRS3618214", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.8967, null, 0.11444, null, 0.66793, null, 0.47524, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Kidney", "Renal System"], [49052, "SRR7633482", "SRX4497213", "SRS3618213", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", null, "pubmed:31158233", null, "G0 pod 03", "GSM3317054", null, "tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G0 mRNA", "G0 pod 03", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish podocyte", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:pod:mCherry|treatment:human APOL1 G0 mRNA", "GSM3317054", "GSM3317054: G0 pod 03; Danio rerio; RNA Seq", "GSM3317054", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317054", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S6_trimmed.fastq.gz", "fastq", 1989842108.0, 39354652.0, "GSM3317054 r1", "0:50.56 1:0", "A:547820589;C:452831323;G:441782569;T:547047192;N:360435", 50, 0, null, null, 547820589, 452831323, 441782569, 547047192, 360435, "SRX4497213", "SRS3618213", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.88797, null, 0.1001, null, 0.67016, null, 0.46755, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Kidney", "Renal System"], [49053, "SRR7633481", "SRX4497212", "SRS3618212", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", null, "pubmed:31158233", null, "G0 pod 02", "GSM3317053", null, "tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G0 mRNA", "G0 pod 02", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish podocyte", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:pod:mCherry|treatment:human APOL1 G0 mRNA", "GSM3317053", "GSM3317053: G0 pod 02; Danio rerio; RNA Seq", "GSM3317053", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317053", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S5_trimmed.fastq.gz", "fastq", 1784099065.0, 35295758.0, "GSM3317053 r1", "0:50.55 1:0", "A:493338451;C:401706697;G:388876128;T:499853218;N:324571", 50, 0, null, null, 493338451, 401706697, 388876128, 499853218, 324571, "SRX4497212", "SRS3618212", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.86757, null, 0.09319, null, 0.6733, null, 0.46511, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Kidney", "Renal System"], [49054, "SRR7633480", "SRX4497211", "SRS3618211", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", null, "pubmed:31158233", null, "G0 pod 01", "GSM3317052", null, "tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G0 mRNA", "G0 pod 01", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish podocyte", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:pod:mCherry|treatment:human APOL1 G0 mRNA", "GSM3317052", "GSM3317052: G0 pod 01; Danio rerio; RNA Seq", "GSM3317052", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317052", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S4_trimmed.fastq.gz", "fastq", 1294942611.0, 25649695.0, "GSM3317052 r1", "0:50.49 1:0", "A:358939215;C:292943376;G:284204779;T:358621256;N:233985", 50, 0, null, null, 358939215, 292943376, 284204779, 358621256, 233985, "SRX4497211", "SRS3618211", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.89677, null, 0.09742, null, 0.66695, null, 0.46036, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Kidney", "Renal System"], [49055, "SRR7633479", "SRX4497210", "SRS3618210", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", null, "pubmed:31158233", null, "control pod 03", "GSM3317051", null, "tissue:zebrafish podocyte|line:pod:mCherry|treatment:control", "control pod 03", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish podocyte", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:pod:mCherry|treatment:control", "GSM3317051", "GSM3317051: control pod 03; Danio rerio; RNA Seq", "GSM3317051", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317051", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S3_trimmed.fastq.gz", "fastq", 1864996530.0, 36896407.0, "GSM3317051 r1", "0:50.55 1:0", "A:514542102;C:423583183;G:412707586;T:513826127;N:337532", 50, 0, null, null, 514542102, 423583183, 412707586, 513826127, 337532, "SRX4497210", "SRS3618210", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.89167, null, 0.10091, null, 0.67773, null, 0.48093, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Kidney", "Renal System"], [49056, "SRR7633478", "SRX4497209", "SRS3618209", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", null, "pubmed:31158233", null, "control pod 02", "GSM3317050", null, "tissue:zebrafish podocyte|line:pod:mCherry|treatment:control", "control pod 02", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish podocyte", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:pod:mCherry|treatment:control", "GSM3317050", "GSM3317050: control pod 02; Danio rerio; RNA Seq", "GSM3317050", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317050", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S2_trimmed.fastq.gz", "fastq", 1405360276.0, 27811908.0, "GSM3317050 r1", "0:50.53 1:0", "A:388467227;C:319138771;G:310773160;T:386727396;N:253722", 50, 0, null, null, 388467227, 319138771, 310773160, 386727396, 253722, "SRX4497209", "SRS3618209", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.898, null, 0.10269, null, 0.66967, null, 0.45546, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Kidney", "Renal System"], [49057, "SRR7633477", "SRX4497208", "SRS3618208", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", null, "pubmed:31158233", null, "control pod 01", "GSM3317049", null, "tissue:zebrafish podocyte|line:pod:mCherry|treatment:control", "control pod 01", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish podocyte", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:pod:mCherry|treatment:control", "GSM3317049", "GSM3317049: control pod 01; Danio rerio; RNA Seq", "GSM3317049", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317049", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S1_trimmed.fastq.gz", "fastq", 931525657.0, 18454172.0, "GSM3317049 r1", "0:50.48 1:0", "A:259125695;C:210068089;G:204402139;T:257763012;N:166722", 50, 0, null, null, 259125695, 210068089, 204402139, 257763012, 166722, "SRX4497208", "SRS3618208", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.89072, null, 0.10423, null, 0.67107, null, 0.46057, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "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.", null, null, null, "Model organism or animal sample from Danio rerio", "miRNA WT SVCV", null, "strain:Wild type|age:6 month|sex:pooled male and female|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP192333", null, null, "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, null, null, null, 276414308, 338128957, 380963712, 321185951, 6253, "SRX7068102", "SRS5584514", "SRA986546", "IIM - CSIC|Biotechnology and Aquaculture", "IIM - CSIC", 1, 0.12679, null, 0.0134, null, 0.9931, null, 0.63608, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, null, null, "Model organism or animal sample from Danio rerio", "miRNA WT Control", null, "strain:Wild type|age:6 month|sex:pooled male and female|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP192333", null, null, "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, null, null, null, 252097427, 365291036, 426841004, 347094254, 6463, "SRX7067941", "SRS5584353", "SRA986495", "IIM - CSIC|Biotechnology and Aquaculture", "IIM - CSIC", 1, 0.01783, null, 0.00242, null, 0.99411, null, 0.61368, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, null, null, "AMut3 S16", "GSM4698247", null, "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 30\u00b5m 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\u2019s 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\u00b0C and maintained in accordance with ISU and UCSD IACUC guidelines.", "tissue:kidney marrow|genotype:grna / ", "GSM4698247", "GSM4698247: AMut3 S16; Danio rerio; RNA Seq", "GSM4698247", null, "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 30\u00b5m 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", null, "SRP273930", null, null, "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, null, null, 403133854, 408666497, 390547168, 458402036, 226189, "SRX8838545", "SRS7101853", "SRA1104643", "GEO", "Boolean, Pediatrics, UCSD", 1, 0.88856, null, 0.071, null, 0.7331, null, 0.50274, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, null, null, "AMut2 S15", "GSM4698246", null, "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 30\u00b5m 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\u2019s 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\u00b0C and maintained in accordance with ISU and UCSD IACUC guidelines.", "tissue:kidney marrow|genotype:grna / ", "GSM4698246", "GSM4698246: AMut2 S15; Danio rerio; RNA Seq", "GSM4698246", null, "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 30\u00b5m 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", null, "SRP273930", null, null, "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, null, null, 471753150, 472824626, 455434892, 531926834, 265118, "SRX8838544", "SRS7101852", "SRA1104643", "GEO", "Boolean, Pediatrics, UCSD", 1, 0.88563, null, 0.0647, null, 0.73054, null, 0.51301, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, null, null, "AMut1 S14", "GSM4698245", null, "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 30\u00b5m 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\u2019s 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\u00b0C and maintained in accordance with ISU and UCSD IACUC guidelines.", "tissue:kidney marrow|genotype:grna / ", "GSM4698245", "GSM4698245: AMut1 S14; Danio rerio; RNA Seq", "GSM4698245", null, "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 30\u00b5m 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", null, "SRP273930", null, null, "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, null, null, 382135276, 389342906, 367829537, 436699819, 211106, "SRX8838543", "SRS7101851", "SRA1104643", "GEO", "Boolean, Pediatrics, UCSD", 1, 0.88823, null, 0.07406, null, 0.73062, null, 0.50537, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, null, null, "WT3 S13", "GSM4698244", null, "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 30\u00b5m 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\u2019s 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\u00b0C and maintained in accordance with ISU and UCSD IACUC guidelines.", "tissue:kidney marrow|genotype:WT", "GSM4698244", "GSM4698244: WT3 S13; Danio rerio; RNA Seq", "GSM4698244", null, "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 30\u00b5m 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", null, "SRP273930", null, null, "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, null, null, 423301555, 439721210, 408339976, 491805474, 242609, "SRX8838542", "SRS7101850", "SRA1104643", "GEO", "Boolean, Pediatrics, UCSD", 1, 0.89892, null, 0.06886, null, 0.74408, null, 0.49795, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, null, null, "WT2 S12", "GSM4698243", null, "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 30\u00b5m 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\u2019s 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\u00b0C and maintained in accordance with ISU and UCSD IACUC guidelines.", "tissue:kidney marrow|genotype:WT", "GSM4698243", "GSM4698243: WT2 S12; Danio rerio; RNA Seq", "GSM4698243", null, "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 30\u00b5m 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", null, "SRP273930", null, null, "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, null, null, 405974612, 400305204, 377359541, 453830617, 221726, "SRX8838541", "SRS7101849", "SRA1104643", "GEO", "Boolean, Pediatrics, UCSD", 1, 0.89995, null, 0.07959, null, 0.7429, null, 0.5021, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, null, null, "WT1 S11", "GSM4698242", null, "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 30\u00b5m 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\u2019s 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\u00b0C and maintained in accordance with ISU and UCSD IACUC guidelines.", "tissue:kidney marrow|genotype:WT", "GSM4698242", "GSM4698242: WT1 S11; Danio rerio; RNA Seq", "GSM4698242", null, "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 30\u00b5m 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", null, "SRP273930", null, null, "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, null, null, 445440119, 445993982, 423050638, 503235344, 254865, "SRX8838540", "SRS7101848", "SRA1104643", "GEO", "Boolean, Pediatrics, UCSD", 1, 0.89811, null, 0.07554, null, 0.72908, null, 0.4892, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2020-07-28", "Undetermined", "Undetermined", "Kidney", "Renal System"]], "truncated": false, "filtered_table_rows_count": 144, "expanded_columns": [], "expandable_columns": [], "columns": 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