{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\" 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. 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 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. 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 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. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.", "GEO Accession:GSM2534769", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101756", null, null, "20150717.A-YS4_R1.fastq.gz", "fastq", 4570634754.0, 36274879.0, "GSM2534769 r1", "0:126", "A:1179398927;C:1024363944;G:1239125274;T:1127644877;N:101732", 126, null, null, null, 1179398927, 1024363944, 1239125274, 1127644877, 101732, "SRX2635096", "SRS2043908", "SRA544882", "GEO", "Drummond, Nephrology, Massachusetts General Hospital", 1, 0.93083, null, 0.27465, null, 0.78102, null, 0.70638, 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"], [41905, "SRR5337745", "SRX2635095", "SRS2043907", "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, "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, "F3CTR1.fastq.gz", "0:75.15 1:0", "A:610515696;C:506550058;G:471139873;T:636560130;N:70292", 75, 0, null, null, 610515696, 506550058, 471139873, 636560130, 70292, "SRX4403255", "SRS3557744", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95447, null, 0.0754, null, 0.78066, null, 0.54856, null, 75, 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"], [48946, "SRR7535404", "SRX4403254", "SRS3557743", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample23", "F3CTR2", 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", "F3CTR2 L23", "F3CTR2 L23", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3CTR2.fastq.gz", "fastq", 3106167820.0, 36871227.0, "F3CTR2.fastq.gz", "0:84.24 1:0", "A:844192333;C:713285812;G:657110592;T:891518698;N:60385", 84, 0, null, null, 844192333, 713285812, 657110592, 891518698, 60385, "SRX4403254", "SRS3557743", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.9554, null, 0.06997, null, 0.79275, null, 0.52557, null, 85, 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"], [48947, "SRR7535405", "SRX4403253", "SRS3557742", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample24", "F3CTR3", 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", "F3CTR3 L24", "F3CTR3 L24", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3CTR3.fastq.gz", "fastq", 2619378393.0, 31091747.0, "F3CTR3.fastq.gz", "0:84.25 1:0", "A:699692748;C:600624113;G:564410765;T:754600796;N:49971", 84, 0, null, null, 699692748, 600624113, 564410765, 754600796, 49971, "SRX4403253", "SRS3557742", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95974, null, 0.06076, null, 0.7932, null, 0.54096, null, 85, 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"], [48948, "SRR7535406", "SRX4403252", "SRS3557741", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample25", "F3CTR4", 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", "F3CTR4 L25", "F3CTR4 L25", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3CTR4.fastq.gz", "fastq", 3292260052.0, 39078900.0, "F3CTR4.fastq.gz", "0:84.25 1:0", "A:880017890;C:753064780;G:705989117;T:953125639;N:62626", 84, 0, null, null, 880017890, 753064780, 705989117, 953125639, 62626, "SRX4403252", "SRS3557741", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95321, null, 0.07242, null, 0.75666, null, 0.54587, 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"], [48949, "SRR7535407", "SRX4403251", "SRS3557740", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample26", "F3CTR5", 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", "F3CTR5 L26", "F3CTR5 L26", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3CTR5.fastq.gz", "fastq", 3007976354.0, 35696121.0, "F3CTR5.fastq.gz", "0:84.27 1:0", "A:778578191;C:708292962;G:650565998;T:870481710;N:57493", 84, 0, null, null, 778578191, 708292962, 650565998, 870481710, 57493, "SRX4403251", "SRS3557740", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95344, null, 0.06722, null, 0.7597, null, 0.52143, 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"], [48950, "SRR7535408", "SRX4403250", "SRS3557739", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample27", "F3CTR6", 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", "F3CTR6 L27", "F3CTR6 L27", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3CTR6.fastq.gz", "fastq", 2550867627.0, 31161224.0, "F3CTR6.fastq.gz", "0:81.86 1:0", "A:1115959207;C:419324274;G:453781546;T:561761915;N:40685", 81, 0, null, null, 1115959207, 419324274, 453781546, 561761915, 40685, "SRX4403250", "SRS3557739", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.92888, null, 0.24434, null, 0.77749, null, 0.51629, 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"], [48951, "SRR7535409", "SRX4403249", "SRS3557738", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample28", "F3CTR7", 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", "F3CTR7 L28", "F3CTR7 L28", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3CTR7.fastq.gz", "fastq", 2059768786.0, 24468469.0, "F3CTR7.fastq.gz", "0:84.18 1:0", "A:558059300;C:468460643;G:436031484;T:597176496;N:40863", 84, 0, null, null, 558059300, 468460643, 436031484, 597176496, 40863, "SRX4403249", "SRS3557738", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94686, null, 0.07284, null, 0.77459, null, 0.54014, null, 85, 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"], [48952, "SRR7535410", "SRX4403248", "SRS3557737", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample29", "F3CTR8", 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", "F3CTR8 L29", "F3CTR8 L29", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3CTR8.fastq.gz", "fastq", 3053213414.0, 36279614.0, "F3CTR8.fastq.gz", "0:84.16 1:0", "A:815581740;C:713814496;G:673475187;T:850294355;N:47636", 84, 0, null, null, 815581740, 713814496, 673475187, 850294355, 47636, "SRX4403248", "SRS3557737", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.9571, null, 0.06714, null, 0.75369, null, 0.54721, null, 85, 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"], [48953, "SRR7535411", "SRX4403247", "SRS3557736", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample30", "F3LFL1", 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", "F3LFL1 L30", "F3LFL1 L30", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3LFL1.fastq.gz", "fastq", 2028343411.0, 26987895.0, "F3LFL1.fastq.gz", "0:75.16 1:0", "A:548593649;C:466971074;G:433327481;T:579386722;N:64485", 75, 0, null, null, 548593649, 466971074, 433327481, 579386722, 64485, "SRX4403247", "SRS3557736", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95498, null, 0.0741, null, 0.7895, null, 0.5309, null, 75, 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"], [48954, "SRR7535412", "SRX4403246", "SRS3557735", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample8", "F0CTR8", 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", "F0CTR8 L8", "F0CTR8 L8", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0CTR8.fastq.gz", "fastq", 2222889019.0, 29574868.0, "F0CTR8.fastq.gz", "0:75.16 1:0", "A:596733500;C:518690507;G:486721856;T:620675208;N:67948", 75, 0, null, null, 596733500, 518690507, 486721856, 620675208, 67948, "SRX4403246", "SRS3557735", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95446, null, 0.05545, null, 0.74815, null, 0.51889, null, 74, 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"], [48955, "SRR7535413", "SRX4403245", "SRS3557734", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample7", "F0CTR7", 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", "F0CTR7 L7", "F0CTR7 L7", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0CTR7.fastq.gz", "fastq", 4544318503.0, 53947186.0, "F0CTR7.fastq.gz", "0:84.24 1:0", "A:1292030811;C:991354554;G:942494048;T:1318393334;N:45756", 84, 0, null, null, 1292030811, 991354554, 942494048, 1318393334, 45756, "SRX4403245", "SRS3557734", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.9503, null, 0.06778, null, 0.75743, null, 0.55348, null, 85, 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"], [48956, "SRR7535414", "SRX4403244", "SRS3557733", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample6", "F0CTR6", 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", "F0CTR6 L6", "F0CTR6 L6", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0CTR6.fastq.gz", "fastq", 2358891923.0, 31391321.0, "F0CTR6.fastq.gz", "0:75.14 1:0", "A:685288644;C:509459791;G:472389125;T:691678243;N:76120", 75, 0, null, null, 685288644, 509459791, 472389125, 691678243, 76120, "SRX4403244", "SRS3557733", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94166, null, 0.07795, null, 0.76195, null, 0.53942, null, 75, 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"], [48957, "SRR7535415", "SRX4403243", "SRS3557732", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample5", "F0CTR5", 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", "F0CTR5 L5", "F0CTR5 L5", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0CTR5.fastq.gz", "fastq", 2588676344.0, 30755117.0, "F0CTR5.fastq.gz", "0:84.17 1:0", "A:720655179;C:582123937;G:551878210;T:733977893;N:41125", 84, 0, null, null, 720655179, 582123937, 551878210, 733977893, 41125, "SRX4403243", "SRS3557732", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95586, null, 0.06561, null, 0.7808, null, 0.54698, null, 83, 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"], [48958, "SRR7535416", "SRX4403242", "SRS3557731", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample4", "F0CTR4", 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", "F0CTR4 L4", "F0CTR4 L4", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0CTR4.fastq.gz", "fastq", 2959885275.0, 35175450.0, "F0CTR4.fastq.gz", "0:84.15 1:0", "A:799876836;C:675392846;G:616854860;T:867718008;N:42725", 84, 0, null, null, 799876836, 675392846, 616854860, 867718008, 42725, "SRX4403242", "SRS3557731", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.93974, null, 0.07556, null, 0.76238, null, 0.50131, null, 85, 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"], [48959, "SRR7535417", "SRX4403241", "SRS3557730", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample3", "F0CTR3", 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", "F0CTR3 L3", "F0CTR3 L3", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0CTR3.fastq.gz", "fastq", 3127991402.0, 37019173.0, "F0CTR3.fastq.gz", "0:84.50 1:0", "A:886233117;C:699410395;G:659031655;T:883271353;N:44882", 84, 0, null, null, 886233117, 699410395, 659031655, 883271353, 44882, "SRX4403241", "SRS3557730", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95481, null, 0.06332, null, 0.77818, null, 0.54263, 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"], [48960, "SRR7535418", "SRX4403240", "SRS3557729", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample2", "F0CTR2", 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", "F0CTR2 L2", "F0CTR2 L2", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0CTR2.fastq.gz", "fastq", 4589246236.0, 54480219.0, "F0CTR2.fastq.gz", "0:84.24 1:0", "A:1318726005;C:987643623;G:940290206;T:1342543647;N:42755", 84, 0, null, null, 1318726005, 987643623, 940290206, 1342543647, 42755, "SRX4403240", "SRS3557729", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94686, null, 0.06888, null, 0.76278, null, 0.55045, 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"], [48961, "SRR7535419", "SRX4403239", "SRS3557728", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample1", "F0CTR1", 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", "F0CTR1 L1", "F0CTR1 L1", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0CTR1.fastq.gz", "fastq", 2895973720.0, 34407735.0, "F0CTR1.fastq.gz", "0:84.17 1:0", "A:805217942;C:647195655;G:615425828;T:828086852;N:47443", 84, 0, null, null, 805217942, 647195655, 615425828, 828086852, 47443, "SRX4403239", "SRS3557728", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95771, null, 0.05823, null, 0.75475, null, 0.54018, null, 84, 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"], [48962, "SRR7535420", "SRX4403238", "SRS3557727", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample10", "F0LFL2", 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", "F0LFL2 L10", "F0LFL2 L10", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0LFL2.fastq.gz", "fastq", 2221964224.0, 29564609.0, "F0LFL2.fastq.gz", "0:75.16 1:0", "A:622205890;C:491850489;G:469917376;T:637922036;N:68433", 75, 0, null, null, 622205890, 491850489, 469917376, 637922036, 68433, "SRX4403238", "SRS3557727", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95207, null, 0.06132, null, 0.76404, null, 0.5374, 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"], [48963, "SRR7535421", "SRX4403237", "SRS3557726", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample9", "F0LFL1", 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", "F0LFL1 L9", "F0LFL1 L9", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0LFL1.fastq.gz", "fastq", 3222133895.0, 38154313.0, "F0LFL1.fastq.gz", "0:84.45 1:0", "A:920033678;C:715675242;G:671297913;T:915080329;N:46733", 84, 0, null, null, 920033678, 715675242, 671297913, 915080329, 46733, "SRX4403237", "SRS3557726", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95496, null, 0.07355, null, 0.76644, null, 0.54508, 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"], [48964, "SRR7535422", "SRX4403236", "SRS3557725", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample20", "F0HFL7", 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", "F0HFL7 L20", "F0HFL7 L20", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0HFL7.fastq.gz", "fastq", 2800528980.0, 33270152.0, "F0HFL7.fastq.gz", "0:84.18 1:0", "A:745732773;C:657771159;G:624594638;T:772385369;N:45041", 84, 0, null, null, 745732773, 657771159, 624594638, 772385369, 45041, "SRX4403236", "SRS3557725", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.9603, null, 0.05557, null, 0.75262, null, 0.53229, null, 83, 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"], [48965, "SRR7535423", "SRX4403235", "SRS3557724", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample19", "F0HFL6", 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", "F0HFL6 L19", "F0HFL6 L19", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0HFL6.fastq.gz", "fastq", 3859582889.0, 45819776.0, "F0HFL6.fastq.gz", "0:84.23 1:0", "A:1042286597;C:895964648;G:843235146;T:1078059877;N:36621", 84, 0, null, null, 1042286597, 895964648, 843235146, 1078059877, 36621, "SRX4403235", "SRS3557724", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95288, null, 0.06929, null, 0.74, null, 0.52268, null, 85, 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"], [48966, "SRR7535424", "SRX4403234", "SRS3557723", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample16", "F0HFL3", 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", "F0HFL3 L16", "F0HFL3 L16", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0HFL3.fastq.gz", "fastq", 3793212903.0, 45071794.0, "F0HFL3.fastq.gz", "0:84.16 1:0", "A:1056360853;C:843514256;G:810627279;T:1082649387;N:61128", 84, 0, null, null, 1056360853, 843514256, 810627279, 1082649387, 61128, "SRX4403234", "SRS3557723", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95323, null, 0.06159, null, 0.76195, null, 0.54295, null, 85, 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"], [48967, "SRR7535425", "SRX4403233", "SRS3557722", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample15", "F0HFL2", 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", "F0HFL2 L15", "F0HFL2 L15", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0HFL2.fastq.gz", "fastq", 1653605409.0, 19670232.0, "F0HFL2.fastq.gz", "0:84.07 1:0", "A:482659933;C:340033054;G:332925206;T:497960425;N:26791", 84, 0, null, null, 482659933, 340033054, 332925206, 497960425, 26791, "SRX4403233", "SRS3557722", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94378, null, 0.07818, null, 0.76654, null, 0.56019, null, 85, 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"], [48968, "SRR7535426", "SRX4403232", "SRS3557721", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample18", "F0HFL5", 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", "F0HFL5 L18", "F0HFL5 L18", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0HFL5.fastq.gz", "fastq", 2841372173.0, 33797215.0, "F0HFL5.fastq.gz", "0:84.07 1:0", "A:778391982;C:632117929;G:585902045;T:844912619;N:47598", 84, 0, null, null, 778391982, 632117929, 585902045, 844912619, 47598, "SRX4403232", "SRS3557721", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.93559, null, 0.07561, null, 0.76895, null, 0.55817, 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"], [48969, "SRR7535427", "SRX4403231", "SRS3557719", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample17", "F0HFL4", 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", "F0HFL4 L17", "F0HFL4 L17", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0HFL4.fastq.gz", "fastq", 3160174261.0, 37565835.0, "F0HFL4.fastq.gz", "0:84.12 1:0", "A:884296991;C:697282059;G:667815635;T:910728716;N:50860", 84, 0, null, null, 884296991, 697282059, 667815635, 910728716, 50860, "SRX4403231", "SRS3557719", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95258, null, 0.06896, null, 0.75753, null, 0.53648, 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"], [48970, "SRR7535428", "SRX4403230", "SRS3557720", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample12", "F0LFL4", 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", "F0LFL4 L12", "F0LFL4 L12", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0LFL4.fastq.gz", "fastq", 2872309444.0, 34017640.0, "F0LFL4.fastq.gz", "0:84.44 1:0", "A:838123566;C:615148814;G:580099793;T:838897200;N:40071", 84, 0, null, null, 838123566, 615148814, 580099793, 838897200, 40071, "SRX4403230", "SRS3557720", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94655, null, 0.07484, null, 0.76055, null, 0.53193, null, 85, 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"], [48971, "SRR7535429", "SRX4403229", "SRS3557718", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample11", "F0LFL3", 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", "F0LFL3 L11", "F0LFL3 L11", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0LFL3.fastq.gz", "fastq", 4819656374.0, 57208863.0, "F0LFL3.fastq.gz", "0:84.25 1:0", "A:1344664833;C:1065935819;G:1021114550;T:1387895714;N:45458", 84, 0, null, null, 1344664833, 1065935819, 1021114550, 1387895714, 45458, "SRX4403229", "SRS3557718", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94968, null, 0.06704, null, 0.75063, null, 0.53941, 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"], [48972, "SRR7535430", "SRX4403228", "SRS3557717", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample14", "F0HFL1", 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", "F0HFL1 L14", "F0HFL1 L14", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0HFL1.fastq.gz", "fastq", 4382160649.0, 58413517.0, "F0HFL1.fastq.gz", "0:75.02 1:0", "A:1369437301;C:861646512;G:809593345;T:1341341422;N:142069", 75, 0, null, null, 1369437301, 861646512, 809593345, 1341341422, 142069, "SRX4403228", "SRS3557717", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.9466, null, 0.08719, null, 0.7794, null, 0.54372, null, 75, 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"], [48973, "SRR7535431", "SRX4403227", "SRS3557716", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample13", "F0LFL5", 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", "F0LFL5 L13", "F0LFL5 L13", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F0LFL5.fastq.gz", "fastq", 4135324561.0, 55077889.0, "F0LFL5.fastq.gz", "0:75.08 1:0", "A:1152758595;C:923324532;G:883060803;T:1176048511;N:132120", 75, 0, null, null, 1152758595, 923324532, 883060803, 1176048511, 132120, "SRX4403227", "SRS3557716", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94936, null, 0.07427, null, 0.7385, null, 0.54293, 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"], [48974, "SRR7535432", "SRX4403226", "SRS3557715", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample38", "F3HFL1", 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", "F3HFL1 L38", "F3HFL1 L38", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3HFL1.fastq.gz", "fastq", 4205002265.0, 49802474.0, "F3HFL1.fastq.gz", "0:84.43 1:0", "A:1296210304;C:849397168;G:835453941;T:1223875076;N:65776", 84, 0, null, null, 1296210304, 849397168, 835453941, 1223875076, 65776, "SRX4403226", "SRS3557715", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95559, null, 0.0917, null, 0.78044, null, 0.61361, null, 85, 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"], [48975, "SRR7535433", "SRX4403225", "SRS3557714", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample37", "F3LFL8", 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", "F3LFL8 L37", "F3LFL8 L37", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3LFL8.fastq.gz", "fastq", 2259705259.0, 26829092.0, "F3LFL8.fastq.gz", "0:84.23 1:0", "A:609862793;C:515167321;G:475663194;T:658969872;N:42079", 84, 0, null, null, 609862793, 515167321, 475663194, 658969872, 42079, "SRX4403225", "SRS3557714", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94002, null, 0.10434, null, 0.75369, null, 0.51155, null, 85, 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"], [48976, "SRR7535434", "SRX4403224", "SRS3557713", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample36", "F3LFL7", 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", "F3LFL7 L36", "F3LFL7 L36", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3LFL7.fastq.gz", "fastq", 2341138815.0, 27781759.0, "F3LFL7.fastq.gz", "0:84.27 1:0", "A:608466569;C:545924123;G:501493228;T:685210306;N:44589", 84, 0, null, null, 608466569, 545924123, 501493228, 685210306, 44589, "SRX4403224", "SRS3557713", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94523, null, 0.08263, null, 0.75284, null, 0.53752, null, 85, 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"], [48977, "SRR7535435", "SRX4403223", "SRS3557712", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample35", "F3LFL6", 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", "F3LFL6 L35", "F3LFL6 L35", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3LFL6.fastq.gz", "fastq", 2937598885.0, 34879736.0, "F3LFL6.fastq.gz", "0:84.22 1:0", "A:782454526;C:678806792;G:617210082;T:859072883;N:54602", 84, 0, null, null, 782454526, 678806792, 617210082, 859072883, 54602, "SRX4403223", "SRS3557712", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94207, null, 0.08495, null, 0.74897, null, 0.5069, null, 85, 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"], [48978, "SRR7535436", "SRX4403222", "SRS3557711", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample34", "F3LFL5", 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", "F3LFL5 L34", "F3LFL5 L34", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3LFL5.fastq.gz", "fastq", 2497066825.0, 29658022.0, "F3LFL5.fastq.gz", "0:84.20 1:0", "A:694874960;C:555774576;G:516525097;T:729844057;N:48135", 84, 0, null, null, 694874960, 555774576, 516525097, 729844057, 48135, "SRX4403222", "SRS3557711", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94238, null, 0.09347, null, 0.76404, null, 0.51048, 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"], [48979, "SRR7535437", "SRX4403221", "SRS3557710", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample33", "F3LFL4", 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", "F3LFL4 L33", "F3LFL4 L33", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3LFL4.fastq.gz", "fastq", 3167171318.0, 37581804.0, "F3LFL4.fastq.gz", "0:84.27 1:0", "A:836474638;C:736638892;G:687417511;T:906580806;N:59471", 84, 0, null, null, 836474638, 736638892, 687417511, 906580806, 59471, "SRX4403221", "SRS3557710", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95381, null, 0.0776, null, 0.74432, null, 0.49786, null, 85, 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"], [48980, "SRR7535438", "SRX4403220", "SRS3557709", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample32", "F3LFL3", 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", "F3LFL3 L32", "F3LFL3 L32", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3LFL3.fastq.gz", "fastq", 3969872568.0, 47103172.0, "F3LFL3.fastq.gz", "0:84.28 1:0", "A:1087899347;C:891968649;G:846315646;T:1143611603;N:77323", 84, 0, null, null, 1087899347, 891968649, 846315646, 1143611603, 77323, "SRX4403220", "SRS3557709", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94717, null, 0.08461, null, 0.74714, null, 0.53355, 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"], [48981, "SRR7535439", "SRX4403219", "SRS3557708", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample31", "F3LFL2", 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", "F3LFL2 L31", "F3LFL2 L31", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3LFL2.fastq.gz", "fastq", 2401613544.0, 31959346.0, "F3LFL2.fastq.gz", "0:75.15 1:0", "A:673230842;C:536445759;G:492980009;T:698882870;N:74064", 75, 0, null, null, 673230842, 536445759, 492980009, 698882870, 74064, "SRX4403219", "SRS3557708", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.95198, null, 0.08486, null, 0.7878, null, 0.55398, null, 75, 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"], [48982, "SRR7535440", "SRX4403218", "SRS3557706", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample40", "F3HFL3", 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", "F3HFL3 L40", "F3HFL3 L40", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3HFL3.fastq.gz", "fastq", 2266960447.0, 26913177.0, "F3HFL3.fastq.gz", "0:84.23 1:0", "A:590021990;C:520283209;G:479594101;T:677024566;N:36581", 84, 0, null, null, 590021990, 520283209, 479594101, 677024566, 36581, "SRX4403218", "SRS3557706", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.94897, null, 0.08251, null, 0.80848, null, 0.57355, null, 85, 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"], [48983, "SRR7535441", "SRX4403217", "SRS3557707", "SRP154295", "PRJNA481502", "Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio", "PRJNA481502", "Transcriptome Analysis", "Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.", null, "pubmed:30530669", null, "sample39", "F3HFL2", 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", "F3HFL2 L39", "F3HFL2 L39", "mRNA seq from total RNA on Illumina Neoprep", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP154295", null, null, "F3HFL2.fastq.gz", "fastq", 2749128323.0, 32649931.0, "F3HFL2.fastq.gz", "0:84.20 1:0", "A:739282939;C:602311637;G:590565979;T:816929591;N:38177", 84, 0, null, null, 739282939, 602311637, 590565979, 816929591, 38177, "SRX4403217", "SRS3557707", "SRA741696", "Gov of Canada", "Gov of Canada", 1, 0.9613, null, 0.09046, null, 0.8104, null, 0.62158, null, 85, 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"], [49049, "SRR7633485", "SRX4497216", "SRS3618216", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2", 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"], [59301, "SRR11851897", "SRX8402007", "SRS6714764", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b ko 3", "GSM4568915", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "scRNA seq gata2b ko 3", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "GSM4568915", "GSM4568915: scRNA seq gata2b ko 3; Danio rerio; RNA Seq", "GSM4568915", null, "1", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "GEO Accession:GSM4568915", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options: appendBCtoName", "KO3_Single_Cell_GAGACGGA.fastq.sorted.fastq.gz", "fastq", 3768784245.0, 63353331.0, "GSM4568915 r1", "0:59.49", "A:1049235928;C:815061845;G:790664763;T:1113812557;N:9152", 59, null, null, null, 1049235928, 815061845, 790664763, 1113812557, 9152, "SRX8402007", "SRS6714764", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.9009, null, 0.07395, null, 0.83524, null, 0.54215, null, 60, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59302, "SRR11851896", "SRX8402006", "SRS6714763", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b ko 2", "GSM4568914", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "scRNA seq gata2b ko 2", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "GSM4568914", "GSM4568914: scRNA seq gata2b ko 2; Danio rerio; RNA Seq", "GSM4568914", null, "1", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "GEO Accession:GSM4568914", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options: appendBCtoName", "KO2_Single_Cell_TTACCTCC.fastq.sorted.fastq.gz", "fastq", 5788926123.0, 96793878.0, "GSM4568914 r1", "0:59.81", "A:1591846184;C:1284226924;G:1217400432;T:1695437315;N:15268", 59, null, null, null, 1591846184, 1284226924, 1217400432, 1695437315, 15268, "SRX8402006", "SRS6714763", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.90311, null, 0.0768, null, 0.82227, null, 0.56806, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59303, "SRR11851895", "SRX8402005", "SRS6714762", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b ko 1", "GSM4568913", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "scRNA seq gata2b ko 1", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko", "GSM4568913", "GSM4568913: scRNA seq gata2b ko 1; Danio rerio; RNA Seq", "GSM4568913", null, "1", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "GEO Accession:GSM4568913", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options: appendBCtoName", "KO1_Single_Cell_TAAGGCTC.fastq.sorted.fastq.gz", "fastq", 4485434923.0, 75329131.0, "GSM4568913 r1", "0:59.54", "A:1245571394;C:1005814804;G:944318855;T:1289711080;N:18790", 59, null, null, null, 1245571394, 1005814804, 944318855, 1289711080, 18790, "SRX8402005", "SRS6714762", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.89937, null, 0.06305, null, 0.83879, null, 0.54954, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59304, "SRR11851894", "SRX8402004", "SRS6714761", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b het 3", "GSM4568912", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "scRNA seq gata2b het 3", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "GSM4568912", "GSM4568912: scRNA seq gata2b het 3; Danio rerio; RNA Seq", "GSM4568912", null, "1", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "GEO Accession:GSM4568912", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options: appendBCtoName", "HET3_Single_Cell_CCTTTACT.fastq.sorted.fastq.gz", "fastq", 3696586389.0, 62109708.0, "GSM4568912 r1", "0:59.52", "A:1054965741;C:827475497;G:744430159;T:1069699165;N:15827", 59, null, null, null, 1054965741, 827475497, 744430159, 1069699165, 15827, "SRX8402004", "SRS6714761", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.89246, null, 0.06392, null, 0.83934, null, 0.56422, null, 58, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59305, "SRR11851893", "SRX8402003", "SRS6714760", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b het 2", "GSM4568911", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "scRNA seq gata2b het 2", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "GSM4568911", "GSM4568911: scRNA seq gata2b het 2; Danio rerio; RNA Seq", "GSM4568911", null, "1", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "GEO Accession:GSM4568911", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options: appendBCtoName", "HET2_Single_Cell_CAGTTATG.fastq.sorted.fastq.gz", "fastq", 5357974983.0, 89558550.0, "GSM4568911 r1", "0:59.83", "A:1490260317;C:1191725100;G:1122517464;T:1553457613;N:14489", 59, null, null, null, 1490260317, 1191725100, 1122517464, 1553457613, 14489, "SRX8402003", "SRS6714760", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.90302, null, 0.07865, null, 0.82603, null, 0.57406, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [59306, "SRR11851892", "SRX8402002", "SRS6714759", "SRP264841", "PRJNA635161", "Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq]", "GSE151231", "Transcriptome Analysis", "Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells.", "parent bioproject:PRJNA635158", "pubmed:34170284", null, "scRNA seq gata2b het 1", "GSM4568910", null, "tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "scRNA seq gata2b het 1", "The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds", "sorted marrow cells", "Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing.", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "Freshly isolated kidney marrow cells from euthanized adult zebrafish.", "cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het", "GSM4568910", "GSM4568910: scRNA seq gata2b het 1; Danio rerio; RNA Seq", "GSM4568910", null, "1", "post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 \u03bcm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops", "GEO Accession:GSM4568910", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP264841", null, "loader:fastq load.py|options: appendBCtoName", "HET1_Single_Cell_ATAGCCTT.fastq.sorted.fastq.gz", "fastq", 4701831804.0, 78923769.0, "GSM4568910 r1", "0:59.57", "A:1307674780;C:1043797904;G:1001646002;T:1348693620;N:19498", 59, null, null, null, 1307674780, 1043797904, 1001646002, 1348693620, 19498, "SRX8402002", "SRS6714759", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.90603, null, 0.07667, null, 0.82704, null, 0.57543, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"]], "truncated": false, "filtered_table_rows_count": 153, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_layout\" = :p0 and \"tissue_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "Renal System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 151, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 150, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "cDNA", "label": "cDNA", "count": 108, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&experiment.library_selection=cDNA", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 43, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&experiment.library_selection=PolyA", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&experiment.library_selection=RANDOM", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 153, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation_coarse=Renal+System", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 150, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&experiment.platform=ILLUMINA", "selected": false}, {"value": "PACBIO_SMRT", "label": "PACBIO_SMRT", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&experiment.platform=PACBIO_SMRT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "Adult", "label": "Adult", "count": 125, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&devstage_curation_coarse=Adult", "selected": false}, {"value": "Larval", "label": "Larval", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&devstage_curation_coarse=Larval", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&devstage_curation_coarse=Undetermined", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "Adult", "label": "Adult", "count": 106, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&devstage_curation=Adult", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 25, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&devstage_curation=Undetermined", "selected": false}, {"value": "Larval", "label": "Larval", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&devstage_curation=Larval", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "Renal System", "label": "Renal System", "count": 153, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "Kidney", "label": "Kidney", "count": 144, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&tissue_curation=Kidney", "selected": false}, {"value": "Marrow", "label": "Marrow", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&tissue_curation=Marrow", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System", "results": [{"value": "unknown", "label": "unknown", "count": 82, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&technology=bulk", "selected": false}, {"value": "indrops", "label": "indrops", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&technology=indrops", "selected": false}, {"value": "smartseq", "label": "smartseq", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&technology=smartseq", "selected": false}, {"value": "generic-scrnaseq-only", "label": "generic-scrnaseq-only", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&technology=generic-scrnaseq-only", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "59306", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Renal+System&_next=59306", "private": false, "allow_execute_sql": true, "query_ms": 121.38289100039401}