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144 rows where experiment.library_layout = "SINGLE" and tissue_curation = "Kidney"

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technology 5

experiment.library_selection 3

devstage_curation_coarse 3

devstage_curation 3

experiment.platform 2

experiment.library_strategy 2

experiment.library_source 2

tissue_curation_coarse 1

tissue_curation 1

  • Kidney · 144 ✖

experiment.library_layout 1

  • SINGLE · 144 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
34960 34960 SRR32588717 SRX27895234 SRS24266236 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 F K   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:kidney|BioSampleModel:Model organism or animal                 Iso Seq RNA from kidney C2 F2 F K C2 F2 F K The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m84270_240904_132604_s1.skera.flnc.fastq.gz fastq 109258150145.0 61126158.0 m84270 240904 132604 s1.skera.flnc.fastq.gz 0:1787.42 A:32153042096;C:22604112467;G:23394852841;T:31106142741;N:0 1787       32153042096 22604112467 23394852841 31106142741 0 SRX27895234 SRS24266236 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Kidney Renal System
34970 34970 SRR32588727 SRX27895224 SRS24266224 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 M K22   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:kidney|BioSampleModel:Model organism or animal                 Iso Seq RNA from kidney C2 F2 M K22 C2 F2 M K22 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m64467e_240829_144745.hifi_reads.flnc.fastq.gz fastq 14838539048.0 3383142.0 m64467e 240829 144745.hifi reads.flnc.fastq.gz 0:4386.02 A:4211191682;C:3185079857;G:3320422646;T:4121844863;N:0 4386       4211191682 3185079857 3320422646 4121844863 0 SRX27895224 SRS24266224 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Kidney Renal System
34971 34971 SRR32588728 SRX27895223 SRS24266234 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 M K21   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:Kidney|BioSampleModel:Model organism or animal                 Iso Seq RNA from kidney C2 F2 M K21 C2 F2 M K21 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m84270_240913_170640_s3.skera.flnc.fastq.gz fastq 100849133955.0 51593887.0 m84270 240913 170640 s3.skera.flnc.fastq.gz 0:1954.67 A:28887816631;C:21568633305;G:22323254809;T:28069429210;N:0 1954       28887816631 21568633305 22323254809 28069429210 0 SRX27895223 SRS24266234 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Kidney Renal System
38296 38296 SRR1647681 SRX756916 SRS742120 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   24K GSM1541905   source name:head kidney|tissue:head kidney|disease state:24h post SVCV infection 24K Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... head kidney   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:head kidney|disease state:24h post SVCV infection GSM1541905 GSM1541905: 24K; Danio rerio; RNA Seq GSM1541905   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541905 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     24K_GTGAAA_L003_R1.fastq fastq 1020487560.0 20009560.0 GSM1541905 r1 0:51 A:266117014;C:246797067;G:240014464;T:267491299;N:67716 51       266117014 246797067 240014464 267491299 67716 SRX756916 SRS742120 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92411   0.07686   0.68647   0.4627   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Kidney Renal System
38297 38297 SRR1647680 SRX756915 SRS742117 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   6K GSM1541904   source name:head kidney|tissue:head kidney|disease state:6h post SVCV infection 6K Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... head kidney   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:head kidney|disease state:6h post SVCV infection GSM1541904 GSM1541904: 6K; Danio rerio; RNA Seq GSM1541904   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541904 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     6K_GTCCGC_L003_R1.fastq fastq 929436036.0 18224236.0 GSM1541904 r1 0:51 A:242005719;C:225485975;G:219890494;T:241993975;N:59873 51       242005719 225485975 219890494 241993975 59873 SRX756915 SRS742117 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92547   0.09105   0.69264   0.49166   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Kidney Renal System
38298 38298 SRR1647679 SRX756914 SRS742116 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   0K GSM1541903   source name:head kidney|tissue:head kidney|disease state:un infected 0K Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... head kidney   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:head kidney|disease state:un infected GSM1541903 GSM1541903: 0K; Danio rerio; RNA Seq GSM1541903   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541903 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     0K_CCGTCC_L003_R1.fastq fastq 1077979095.0 21136845.0 GSM1541903 r1 0:51 A:280277150;C:261348733;G:255721013;T:280562071;N:70128 51       280277150 261348733 255721013 280562071 70128 SRX756914 SRS742116 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92545   0.08181   0.68373   0.49408   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Kidney Renal System
41902 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.   pubmed:28656378   YS6 GSM2534771   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   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.   transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult GSM2534771 GSM2534771: YS6; Danio rerio; RNA Seq GSM2534771   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   SRP101756     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       1185876928 1354521221 1643633065 1249907593 113089 SRX2635098 SRS2043910 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.97351   0.17501   0.85303   0.75625   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41903 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.   pubmed:28656378   YS5 GSM2534770   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   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.   transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult GSM2534770 GSM2534770: YS5; Danio rerio; RNA Seq GSM2534770   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   SRP101756     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       648837532 505738661 568578688 574489076 52101 SRX2635097 SRS2043909 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.94402   0.1927   0.77585   0.67728   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41904 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.   pubmed:28656378   YS4 GSM2534769   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   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.   transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult GSM2534769 GSM2534769: YS4; Danio rerio; RNA Seq GSM2534769   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   SRP101756     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       1179398927 1024363944 1239125274 1127644877 101732 SRX2635096 SRS2043908 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.93083   0.27465   0.78102   0.70638   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41905 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.   pubmed:28656378   YS3 GSM2534768   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   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.   transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult GSM2534768 GSM2534768: YS3; Danio rerio; RNA Seq GSM2534768   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   SRP101756     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       1607436982 1222995706 1369036558 1448805498 123942 SRX2635095 SRS2043907 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.93399   0.20266   0.78076   0.73978   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41906 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.   pubmed:28656378   YS2 GSM2534767   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   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.   transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult GSM2534767 GSM2534767: YS2; Danio rerio; RNA Seq GSM2534767   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   SRP101756     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       1320151433 986429614 1112497899 1261495719 104709 SRX2635094 SRS2043906 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.91952   0.24724   0.73884   0.63985   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41907 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.   pubmed:28656378   YS1 GSM2534766   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   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.   transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult GSM2534766 GSM2534766: YS1; Danio rerio; RNA Seq GSM2534766   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   SRP101756     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       1521231890 1760818628 2148863730 1569634203 155441 SRX2635093 SRS2043905 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.96016   0.1982   0.86261   0.75572   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
42599 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   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   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.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   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   SRP111339     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     6573828142 5137891481 5021324431 6582457296 352238 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.83828   0.08537   0.83552   0.56658   61   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42600 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   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   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.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   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   SRP111339     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     743619897 720488231 1031094190 562297818 316728 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42601 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   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   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.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   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   SRP111339     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       913664473 577895371 646194239 918893384 1169397 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42602 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   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   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.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   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   SRP111339     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       1351470715 1294400719 1379073889 1322397488 3836701 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       14   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42603 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   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   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.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   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   SRP111339     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     7598044404 5948542485 5746339343 7575168754 276053 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.83437   0.08222   0.82658   0.54569   61   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42604 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   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   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.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   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   SRP111339     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     892841722 781074758 1176856476 672376743 571093 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42605 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   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   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.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   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   SRP111339     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       1016854893 682256486 759860179 1063129659 1619575 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42606 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   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   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.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   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   SRP111339     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       1513770161 1469643118 1669791951 1509862301 3443855 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       14   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42607 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 GSM2696102   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   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.   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   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   SRP111339     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     506372087 413396954 415448050 652683387 28918 SRX2989235 SRS2341158 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.86587   0.12447   0.80336   0.54126   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42608 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 GSM2696102   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   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.   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   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   SRP111339     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     554483675 506568509 721419849 974751566 3789451 SRX2989235 SRS2341158 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.00796   0.0077   0.99961   0.78947   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42609 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 GSM2696101   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   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.   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   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   SRP111339     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     402261661 326108405 319637981 501413963 20726 SRX2989234 SRS2341157 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.84263   0.11449   0.79464   0.57001   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42610 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 GSM2696101   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   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.   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   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   SRP111339     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     432547886 403759182 561234660 751564536 2897536 SRX2989234 SRS2341157 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.00796   0.00773   0.99971   0.82758   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42611 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #2 GSM2696100   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   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.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696100 GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq GSM2696100   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   SRP111339     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     821476951 657776656 665293293 1057448635 46965 SRX2989233 SRS2341156 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.84222   0.12969   0.80683   0.53542   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42612 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #2 GSM2696100   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   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.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696100 GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq GSM2696100   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   SRP111339     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     880464480 827380868 1171423978 1561925150 6086774 SRX2989233 SRS2341156 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.00782   0.0075   0.99947   0.91666   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42613 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #1 GSM2696099   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   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.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696099 GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq GSM2696099   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   SRP111339     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     858288917 693848400 675650809 1085369048 48322 SRX2989232 SRS2341155 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.8771   0.13918   0.81115   0.59004   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42614 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 … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #1 GSM2696099   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   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.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696099 GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq GSM2696099   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   SRP111339     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     914884703 856837987 1192418010 1631240786 6292814 SRX2989232 SRS2341155 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0063   0.00598   0.99959   0.8913   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
47595 47595 SRR6661145 SRX3638241 SRS2904492 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWTPHZ 3 GSM2975189   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWTPHZ 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975189 GSM2975189: KidWTPHZ 3; Danio rerio; RNA Seq GSM2975189   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975189 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWTPHZ_3.fastq.gz fastq 858099990.0 16825490.0 GSM2975189 r1 0:51 A:231903062;C:197865548;G:200825484;T:227491985;N:13911 51       231903062 197865548 200825484 227491985 13911 SRX3638241 SRS2904492 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.9605   0.10316   0.70721   0.51089   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47596 47596 SRR6661144 SRX3638240 SRS2904491 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWTPHZ 2 GSM2975188   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWTPHZ 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975188 GSM2975188: KidWTPHZ 2; Danio rerio; RNA Seq GSM2975188   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975188 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWTPHZ_2.fastq.gz fastq 799571013.0 15677863.0 GSM2975188 r1 0:51 A:217401512;C:183178629;G:185275617;T:213702318;N:12937 51       217401512 183178629 185275617 213702318 12937 SRX3638240 SRS2904491 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.96209   0.10882   0.70861   0.5149   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47597 47597 SRR6661143 SRX3638239 SRS2904490 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWTPHZ 1 GSM2975187   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWTPHZ 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975187 GSM2975187: KidWTPHZ 1; Danio rerio; RNA Seq GSM2975187   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975187 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWTPHZ_1.fastq.gz fastq 816038505.0 16000755.0 GSM2975187 r1 0:51 A:218420574;C:190260181;G:192288409;T:215056318;N:13023 51       218420574 190260181 192288409 215056318 13023 SRX3638239 SRS2904490 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.96264   0.09527   0.70834   0.51477   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47598 47598 SRR6661142 SRX3638238 SRS2904489 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWT 3 GSM2975186   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWT 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975186 GSM2975186: KidWT 3; Danio rerio; RNA Seq GSM2975186   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975186 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWT_3.fastq.gz fastq 852094026.0 16707726.0 GSM2975186 r1 0:51 A:234167802;C:192807979;G:194651214;T:230453461;N:13570 51       234167802 192807979 194651214 230453461 13570 SRX3638238 SRS2904489 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.95788   0.12336   0.70258   0.48964   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47599 47599 SRR6661141 SRX3638237 SRS2904488 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWT 2 GSM2975185   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWT 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975185 GSM2975185: KidWT 2; Danio rerio; RNA Seq GSM2975185   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975185 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWT_2.fastq.gz fastq 969772038.0 19015138.0 GSM2975185 r1 0:51 A:265582126;C:219526888;G:222468938;T:262178447;N:15639 51       265582126 219526888 222468938 262178447 15639 SRX3638237 SRS2904488 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.95803   0.12522   0.69794   0.50805   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47600 47600 SRR6661140 SRX3638236 SRS2904487 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWT 1 GSM2975184   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWT 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975184 GSM2975184: KidWT 1; Danio rerio; RNA Seq GSM2975184   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975184 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWT_1.fastq.gz fastq 815590011.0 15991961.0 GSM2975184 r1 0:51 A:224190865;C:184406547;G:186159880;T:220819162;N:13557 51       224190865 184406547 186159880 220819162 13557 SRX3638236 SRS2904487 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.95883   0.13181   0.7023   0.49523   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47601 47601 SRR6661139 SRX3638235 SRS2904486 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKOPHZ 3 GSM2975183   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKOPHZ 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975183 GSM2975183: KidDKOPHZ 3; Danio rerio; RNA Seq GSM2975183   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975183 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKOPHZ_3.fastq.gz fastq 789588885.0 15482135.0 GSM2975183 r1 0:51 A:215354577;C:180286176;G:181162894;T:212772248;N:12990 51       215354577 180286176 181162894 212772248 12990 SRX3638235 SRS2904486 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.92385   0.10405   0.70471   0.50985   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47602 47602 SRR6661138 SRX3638234 SRS2904485 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKOPHZ 2 GSM2975182   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKOPHZ 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975182 GSM2975182: KidDKOPHZ 2; Danio rerio; RNA Seq GSM2975182   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975182 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKOPHZ_2.fastq.gz fastq 866844552.0 16996952.0 GSM2975182 r1 0:51 A:235445628;C:198901971;G:200334068;T:232148841;N:14044 51       235445628 198901971 200334068 232148841 14044 SRX3638234 SRS2904485 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.92657   0.10886   0.71112   0.52093   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47603 47603 SRR6661137 SRX3638233 SRS2904484 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKOPHZ 1 GSM2975181   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKOPHZ 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975181 GSM2975181: KidDKOPHZ 1; Danio rerio; RNA Seq GSM2975181   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975181 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKOPHZ_1.fastq.gz fastq 795526560.0 15598560.0 GSM2975181 r1 0:51 A:216666052;C:181785239;G:183159054;T:213903089;N:13126 51       216666052 181785239 183159054 213903089 13126 SRX3638233 SRS2904484 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.92522   0.10277   0.7121   0.51721   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47604 47604 SRR6661136 SRX3638232 SRS2904483 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKO 3 GSM2975180   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKO 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975180 GSM2975180: KidDKO 3; Danio rerio; RNA Seq GSM2975180   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975180 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKO_3.fastq.gz fastq 699170577.0 13709227.0 GSM2975180 r1 0:51 A:191094810;C:157413925;G:158857752;T:191792628;N:11462 51       191094810 157413925 158857752 191792628 11462 SRX3638232 SRS2904483 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.9183   0.12207   0.7083   0.52994   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47605 47605 SRR6661135 SRX3638231 SRS2904482 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKO 2 GSM2975179   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKO 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975179 GSM2975179: KidDKO 2; Danio rerio; RNA Seq GSM2975179   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975179 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKO_2.fastq.gz fastq 720757194.0 14132494.0 GSM2975179 r1 0:51 A:198433339;C:163064446;G:163967236;T:195280391;N:11782 51       198433339 163064446 163967236 195280391 11782 SRX3638231 SRS2904482 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.92921   0.11261   0.7063   0.52644   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47606 47606 SRR6661134 SRX3638230 SRS2904481 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKO 1 GSM2975178   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKO 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975178 GSM2975178: KidDKO 1; Danio rerio; RNA Seq GSM2975178   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975178 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKO_1.fastq.gz fastq 835548606.0 16383306.0 GSM2975178 r1 0:51 A:227900020;C:191118125;G:192603640;T:223913065;N:13756 51       227900020 191118125 192603640 223913065 13756 SRX3638230 SRS2904481 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.93166   0.10926   0.7063   0.50705   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
48941 48941 SRR7535399 SRX4403259 SRS3557748 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample43 F3HFL6   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3HFL6 L43 F3HFL6 L43 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3HFL6.fastq.gz fastq 3513906206.0 41769622.0 F3HFL6.fastq.gz 0:84.13 1:0 A:977114573;C:787720805;G:749651347;T:999364818;N:54663 84 0     977114573 787720805 749651347 999364818 54663 SRX4403259 SRS3557748 SRA741696 Gov of Canada Gov of Canada 1 0.95671   0.06506   0.78228   0.56305   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48942 48942 SRR7535400 SRX4403258 SRS3557747 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample41 F3HFL4   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3HFL4 L41 F3HFL4 L41 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3HFL4.fastq.gz fastq 1925799513.0 22885356.0 F3HFL4.fastq.gz 0:84.15 1:0 A:524298249;C:430610288;G:398055851;T:572803437;N:31688 84 0     524298249 430610288 398055851 572803437 31688 SRX4403258 SRS3557747 SRA741696 Gov of Canada Gov of Canada 1 0.93737   0.10113   0.81022   0.55692   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48943 48943 SRR7535401 SRX4403257 SRS3557746 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample42 F3HFL5   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3HFL5 L42 F3HFL5 L42 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3HFL5.fastq.gz fastq 2861742645.0 33977477.0 F3HFL5.fastq.gz 0:84.22 1:0 A:771306767;C:644570838;G:600324085;T:845486554;N:54401 84 0     771306767 644570838 600324085 845486554 54401 SRX4403257 SRS3557746 SRA741696 Gov of Canada Gov of Canada 1 0.95145   0.08188   0.78084   0.53906   82   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-07-18 Adult Adult Kidney Renal System
48944 48944 SRR7535402 SRX4403256 SRS3557745 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample21 F0HFL8   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0HFL8 L21 F0HFL8 L21 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0HFL8.fastq.gz fastq 3270195567.0 43558704.0 F0HFL8.fastq.gz 0:75.08 1:0 A:931015183;C:710121529;G:674934313;T:954020799;N:103743 75 0     931015183 710121529 674934313 954020799 103743 SRX4403256 SRS3557745 SRA741696 Gov of Canada Gov of Canada 1 0.94496   0.07696   0.74931   0.55469   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48945 48945 SRR7535403 SRX4403255 SRS3557744 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample22 F3CTR1   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3CTR1 L22 F3CTR1 L22 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3CTR1.fastq.gz fastq 2224836049.0 29606943.0 F3CTR1.fastq.gz 0:75.15 1:0 A:610515696;C:506550058;G:471139873;T:636560130;N:70292 75 0     610515696 506550058 471139873 636560130 70292 SRX4403255 SRS3557744 SRA741696 Gov of Canada Gov of Canada 1 0.95447   0.0754   0.78066   0.54856   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48946 48946 SRR7535404 SRX4403254 SRS3557743 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample23 F3CTR2   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3CTR2 L23 F3CTR2 L23 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3CTR2.fastq.gz fastq 3106167820.0 36871227.0 F3CTR2.fastq.gz 0:84.24 1:0 A:844192333;C:713285812;G:657110592;T:891518698;N:60385 84 0     844192333 713285812 657110592 891518698 60385 SRX4403254 SRS3557743 SRA741696 Gov of Canada Gov of Canada 1 0.9554   0.06997   0.79275   0.52557   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48947 48947 SRR7535405 SRX4403253 SRS3557742 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample24 F3CTR3   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3CTR3 L24 F3CTR3 L24 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3CTR3.fastq.gz fastq 2619378393.0 31091747.0 F3CTR3.fastq.gz 0:84.25 1:0 A:699692748;C:600624113;G:564410765;T:754600796;N:49971 84 0     699692748 600624113 564410765 754600796 49971 SRX4403253 SRS3557742 SRA741696 Gov of Canada Gov of Canada 1 0.95974   0.06076   0.7932   0.54096   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48948 48948 SRR7535406 SRX4403252 SRS3557741 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample25 F3CTR4   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3CTR4 L25 F3CTR4 L25 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3CTR4.fastq.gz fastq 3292260052.0 39078900.0 F3CTR4.fastq.gz 0:84.25 1:0 A:880017890;C:753064780;G:705989117;T:953125639;N:62626 84 0     880017890 753064780 705989117 953125639 62626 SRX4403252 SRS3557741 SRA741696 Gov of Canada Gov of Canada 1 0.95321   0.07242   0.75666   0.54587   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48949 48949 SRR7535407 SRX4403251 SRS3557740 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample26 F3CTR5   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3CTR5 L26 F3CTR5 L26 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3CTR5.fastq.gz fastq 3007976354.0 35696121.0 F3CTR5.fastq.gz 0:84.27 1:0 A:778578191;C:708292962;G:650565998;T:870481710;N:57493 84 0     778578191 708292962 650565998 870481710 57493 SRX4403251 SRS3557740 SRA741696 Gov of Canada Gov of Canada 1 0.95344   0.06722   0.7597   0.52143   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48950 48950 SRR7535408 SRX4403250 SRS3557739 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample27 F3CTR6   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3CTR6 L27 F3CTR6 L27 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3CTR6.fastq.gz fastq 2550867627.0 31161224.0 F3CTR6.fastq.gz 0:81.86 1:0 A:1115959207;C:419324274;G:453781546;T:561761915;N:40685 81 0     1115959207 419324274 453781546 561761915 40685 SRX4403250 SRS3557739 SRA741696 Gov of Canada Gov of Canada 1 0.92888   0.24434   0.77749   0.51629   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48951 48951 SRR7535409 SRX4403249 SRS3557738 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample28 F3CTR7   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3CTR7 L28 F3CTR7 L28 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3CTR7.fastq.gz fastq 2059768786.0 24468469.0 F3CTR7.fastq.gz 0:84.18 1:0 A:558059300;C:468460643;G:436031484;T:597176496;N:40863 84 0     558059300 468460643 436031484 597176496 40863 SRX4403249 SRS3557738 SRA741696 Gov of Canada Gov of Canada 1 0.94686   0.07284   0.77459   0.54014   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48952 48952 SRR7535410 SRX4403248 SRS3557737 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample29 F3CTR8   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3CTR8 L29 F3CTR8 L29 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3CTR8.fastq.gz fastq 3053213414.0 36279614.0 F3CTR8.fastq.gz 0:84.16 1:0 A:815581740;C:713814496;G:673475187;T:850294355;N:47636 84 0     815581740 713814496 673475187 850294355 47636 SRX4403248 SRS3557737 SRA741696 Gov of Canada Gov of Canada 1 0.9571   0.06714   0.75369   0.54721   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48953 48953 SRR7535411 SRX4403247 SRS3557736 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample30 F3LFL1   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3LFL1 L30 F3LFL1 L30 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3LFL1.fastq.gz fastq 2028343411.0 26987895.0 F3LFL1.fastq.gz 0:75.16 1:0 A:548593649;C:466971074;G:433327481;T:579386722;N:64485 75 0     548593649 466971074 433327481 579386722 64485 SRX4403247 SRS3557736 SRA741696 Gov of Canada Gov of Canada 1 0.95498   0.0741   0.7895   0.5309   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-07-18 Adult Adult Kidney Renal System
48954 48954 SRR7535412 SRX4403246 SRS3557735 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample8 F0CTR8   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0CTR8 L8 F0CTR8 L8 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0CTR8.fastq.gz fastq 2222889019.0 29574868.0 F0CTR8.fastq.gz 0:75.16 1:0 A:596733500;C:518690507;G:486721856;T:620675208;N:67948 75 0     596733500 518690507 486721856 620675208 67948 SRX4403246 SRS3557735 SRA741696 Gov of Canada Gov of Canada 1 0.95446   0.05545   0.74815   0.51889   74   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48955 48955 SRR7535413 SRX4403245 SRS3557734 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample7 F0CTR7   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0CTR7 L7 F0CTR7 L7 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0CTR7.fastq.gz fastq 4544318503.0 53947186.0 F0CTR7.fastq.gz 0:84.24 1:0 A:1292030811;C:991354554;G:942494048;T:1318393334;N:45756 84 0     1292030811 991354554 942494048 1318393334 45756 SRX4403245 SRS3557734 SRA741696 Gov of Canada Gov of Canada 1 0.9503   0.06778   0.75743   0.55348   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-07-18 Adult Adult Kidney Renal System
48956 48956 SRR7535414 SRX4403244 SRS3557733 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample6 F0CTR6   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0CTR6 L6 F0CTR6 L6 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0CTR6.fastq.gz fastq 2358891923.0 31391321.0 F0CTR6.fastq.gz 0:75.14 1:0 A:685288644;C:509459791;G:472389125;T:691678243;N:76120 75 0     685288644 509459791 472389125 691678243 76120 SRX4403244 SRS3557733 SRA741696 Gov of Canada Gov of Canada 1 0.94166   0.07795   0.76195   0.53942   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48957 48957 SRR7535415 SRX4403243 SRS3557732 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample5 F0CTR5   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0CTR5 L5 F0CTR5 L5 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0CTR5.fastq.gz fastq 2588676344.0 30755117.0 F0CTR5.fastq.gz 0:84.17 1:0 A:720655179;C:582123937;G:551878210;T:733977893;N:41125 84 0     720655179 582123937 551878210 733977893 41125 SRX4403243 SRS3557732 SRA741696 Gov of Canada Gov of Canada 1 0.95586   0.06561   0.7808   0.54698   83   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48958 48958 SRR7535416 SRX4403242 SRS3557731 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample4 F0CTR4   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0CTR4 L4 F0CTR4 L4 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0CTR4.fastq.gz fastq 2959885275.0 35175450.0 F0CTR4.fastq.gz 0:84.15 1:0 A:799876836;C:675392846;G:616854860;T:867718008;N:42725 84 0     799876836 675392846 616854860 867718008 42725 SRX4403242 SRS3557731 SRA741696 Gov of Canada Gov of Canada 1 0.93974   0.07556   0.76238   0.50131   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48959 48959 SRR7535417 SRX4403241 SRS3557730 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample3 F0CTR3   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0CTR3 L3 F0CTR3 L3 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0CTR3.fastq.gz fastq 3127991402.0 37019173.0 F0CTR3.fastq.gz 0:84.50 1:0 A:886233117;C:699410395;G:659031655;T:883271353;N:44882 84 0     886233117 699410395 659031655 883271353 44882 SRX4403241 SRS3557730 SRA741696 Gov of Canada Gov of Canada 1 0.95481   0.06332   0.77818   0.54263   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48960 48960 SRR7535418 SRX4403240 SRS3557729 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample2 F0CTR2   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0CTR2 L2 F0CTR2 L2 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0CTR2.fastq.gz fastq 4589246236.0 54480219.0 F0CTR2.fastq.gz 0:84.24 1:0 A:1318726005;C:987643623;G:940290206;T:1342543647;N:42755 84 0     1318726005 987643623 940290206 1342543647 42755 SRX4403240 SRS3557729 SRA741696 Gov of Canada Gov of Canada 1 0.94686   0.06888   0.76278   0.55045   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48961 48961 SRR7535419 SRX4403239 SRS3557728 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample1 F0CTR1   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0CTR1 L1 F0CTR1 L1 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0CTR1.fastq.gz fastq 2895973720.0 34407735.0 F0CTR1.fastq.gz 0:84.17 1:0 A:805217942;C:647195655;G:615425828;T:828086852;N:47443 84 0     805217942 647195655 615425828 828086852 47443 SRX4403239 SRS3557728 SRA741696 Gov of Canada Gov of Canada 1 0.95771   0.05823   0.75475   0.54018   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-07-18 Adult Adult Kidney Renal System
48962 48962 SRR7535420 SRX4403238 SRS3557727 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample10 F0LFL2   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0LFL2 L10 F0LFL2 L10 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0LFL2.fastq.gz fastq 2221964224.0 29564609.0 F0LFL2.fastq.gz 0:75.16 1:0 A:622205890;C:491850489;G:469917376;T:637922036;N:68433 75 0     622205890 491850489 469917376 637922036 68433 SRX4403238 SRS3557727 SRA741696 Gov of Canada Gov of Canada 1 0.95207   0.06132   0.76404   0.5374   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48963 48963 SRR7535421 SRX4403237 SRS3557726 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample9 F0LFL1   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0LFL1 L9 F0LFL1 L9 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0LFL1.fastq.gz fastq 3222133895.0 38154313.0 F0LFL1.fastq.gz 0:84.45 1:0 A:920033678;C:715675242;G:671297913;T:915080329;N:46733 84 0     920033678 715675242 671297913 915080329 46733 SRX4403237 SRS3557726 SRA741696 Gov of Canada Gov of Canada 1 0.95496   0.07355   0.76644   0.54508   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48964 48964 SRR7535422 SRX4403236 SRS3557725 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample20 F0HFL7   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0HFL7 L20 F0HFL7 L20 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0HFL7.fastq.gz fastq 2800528980.0 33270152.0 F0HFL7.fastq.gz 0:84.18 1:0 A:745732773;C:657771159;G:624594638;T:772385369;N:45041 84 0     745732773 657771159 624594638 772385369 45041 SRX4403236 SRS3557725 SRA741696 Gov of Canada Gov of Canada 1 0.9603   0.05557   0.75262   0.53229   83   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48965 48965 SRR7535423 SRX4403235 SRS3557724 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample19 F0HFL6   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0HFL6 L19 F0HFL6 L19 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0HFL6.fastq.gz fastq 3859582889.0 45819776.0 F0HFL6.fastq.gz 0:84.23 1:0 A:1042286597;C:895964648;G:843235146;T:1078059877;N:36621 84 0     1042286597 895964648 843235146 1078059877 36621 SRX4403235 SRS3557724 SRA741696 Gov of Canada Gov of Canada 1 0.95288   0.06929   0.74   0.52268   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48966 48966 SRR7535424 SRX4403234 SRS3557723 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample16 F0HFL3   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0HFL3 L16 F0HFL3 L16 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0HFL3.fastq.gz fastq 3793212903.0 45071794.0 F0HFL3.fastq.gz 0:84.16 1:0 A:1056360853;C:843514256;G:810627279;T:1082649387;N:61128 84 0     1056360853 843514256 810627279 1082649387 61128 SRX4403234 SRS3557723 SRA741696 Gov of Canada Gov of Canada 1 0.95323   0.06159   0.76195   0.54295   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48967 48967 SRR7535425 SRX4403233 SRS3557722 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample15 F0HFL2   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0HFL2 L15 F0HFL2 L15 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0HFL2.fastq.gz fastq 1653605409.0 19670232.0 F0HFL2.fastq.gz 0:84.07 1:0 A:482659933;C:340033054;G:332925206;T:497960425;N:26791 84 0     482659933 340033054 332925206 497960425 26791 SRX4403233 SRS3557722 SRA741696 Gov of Canada Gov of Canada 1 0.94378   0.07818   0.76654   0.56019   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48968 48968 SRR7535426 SRX4403232 SRS3557721 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample18 F0HFL5   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0HFL5 L18 F0HFL5 L18 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0HFL5.fastq.gz fastq 2841372173.0 33797215.0 F0HFL5.fastq.gz 0:84.07 1:0 A:778391982;C:632117929;G:585902045;T:844912619;N:47598 84 0     778391982 632117929 585902045 844912619 47598 SRX4403232 SRS3557721 SRA741696 Gov of Canada Gov of Canada 1 0.93559   0.07561   0.76895   0.55817   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48969 48969 SRR7535427 SRX4403231 SRS3557719 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample17 F0HFL4   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0HFL4 L17 F0HFL4 L17 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0HFL4.fastq.gz fastq 3160174261.0 37565835.0 F0HFL4.fastq.gz 0:84.12 1:0 A:884296991;C:697282059;G:667815635;T:910728716;N:50860 84 0     884296991 697282059 667815635 910728716 50860 SRX4403231 SRS3557719 SRA741696 Gov of Canada Gov of Canada 1 0.95258   0.06896   0.75753   0.53648   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48970 48970 SRR7535428 SRX4403230 SRS3557720 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample12 F0LFL4   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0LFL4 L12 F0LFL4 L12 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0LFL4.fastq.gz fastq 2872309444.0 34017640.0 F0LFL4.fastq.gz 0:84.44 1:0 A:838123566;C:615148814;G:580099793;T:838897200;N:40071 84 0     838123566 615148814 580099793 838897200 40071 SRX4403230 SRS3557720 SRA741696 Gov of Canada Gov of Canada 1 0.94655   0.07484   0.76055   0.53193   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48971 48971 SRR7535429 SRX4403229 SRS3557718 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample11 F0LFL3   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0LFL3 L11 F0LFL3 L11 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0LFL3.fastq.gz fastq 4819656374.0 57208863.0 F0LFL3.fastq.gz 0:84.25 1:0 A:1344664833;C:1065935819;G:1021114550;T:1387895714;N:45458 84 0     1344664833 1065935819 1021114550 1387895714 45458 SRX4403229 SRS3557718 SRA741696 Gov of Canada Gov of Canada 1 0.94968   0.06704   0.75063   0.53941   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48972 48972 SRR7535430 SRX4403228 SRS3557717 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample14 F0HFL1   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0HFL1 L14 F0HFL1 L14 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0HFL1.fastq.gz fastq 4382160649.0 58413517.0 F0HFL1.fastq.gz 0:75.02 1:0 A:1369437301;C:861646512;G:809593345;T:1341341422;N:142069 75 0     1369437301 861646512 809593345 1341341422 142069 SRX4403228 SRS3557717 SRA741696 Gov of Canada Gov of Canada 1 0.9466   0.08719   0.7794   0.54372   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-07-18 Adult Adult Kidney Renal System
48973 48973 SRR7535431 SRX4403227 SRS3557716 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample13 F0LFL5   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F0LFL5 L13 F0LFL5 L13 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F0LFL5.fastq.gz fastq 4135324561.0 55077889.0 F0LFL5.fastq.gz 0:75.08 1:0 A:1152758595;C:923324532;G:883060803;T:1176048511;N:132120 75 0     1152758595 923324532 883060803 1176048511 132120 SRX4403227 SRS3557716 SRA741696 Gov of Canada Gov of Canada 1 0.94936   0.07427   0.7385   0.54293   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48974 48974 SRR7535432 SRX4403226 SRS3557715 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample38 F3HFL1   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3HFL1 L38 F3HFL1 L38 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3HFL1.fastq.gz fastq 4205002265.0 49802474.0 F3HFL1.fastq.gz 0:84.43 1:0 A:1296210304;C:849397168;G:835453941;T:1223875076;N:65776 84 0     1296210304 849397168 835453941 1223875076 65776 SRX4403226 SRS3557715 SRA741696 Gov of Canada Gov of Canada 1 0.95559   0.0917   0.78044   0.61361   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48975 48975 SRR7535433 SRX4403225 SRS3557714 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample37 F3LFL8   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3LFL8 L37 F3LFL8 L37 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3LFL8.fastq.gz fastq 2259705259.0 26829092.0 F3LFL8.fastq.gz 0:84.23 1:0 A:609862793;C:515167321;G:475663194;T:658969872;N:42079 84 0     609862793 515167321 475663194 658969872 42079 SRX4403225 SRS3557714 SRA741696 Gov of Canada Gov of Canada 1 0.94002   0.10434   0.75369   0.51155   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48976 48976 SRR7535434 SRX4403224 SRS3557713 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample36 F3LFL7   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3LFL7 L36 F3LFL7 L36 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3LFL7.fastq.gz fastq 2341138815.0 27781759.0 F3LFL7.fastq.gz 0:84.27 1:0 A:608466569;C:545924123;G:501493228;T:685210306;N:44589 84 0     608466569 545924123 501493228 685210306 44589 SRX4403224 SRS3557713 SRA741696 Gov of Canada Gov of Canada 1 0.94523   0.08263   0.75284   0.53752   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48977 48977 SRR7535435 SRX4403223 SRS3557712 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample35 F3LFL6   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3LFL6 L35 F3LFL6 L35 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3LFL6.fastq.gz fastq 2937598885.0 34879736.0 F3LFL6.fastq.gz 0:84.22 1:0 A:782454526;C:678806792;G:617210082;T:859072883;N:54602 84 0     782454526 678806792 617210082 859072883 54602 SRX4403223 SRS3557712 SRA741696 Gov of Canada Gov of Canada 1 0.94207   0.08495   0.74897   0.5069   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48978 48978 SRR7535436 SRX4403222 SRS3557711 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample34 F3LFL5   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3LFL5 L34 F3LFL5 L34 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3LFL5.fastq.gz fastq 2497066825.0 29658022.0 F3LFL5.fastq.gz 0:84.20 1:0 A:694874960;C:555774576;G:516525097;T:729844057;N:48135 84 0     694874960 555774576 516525097 729844057 48135 SRX4403222 SRS3557711 SRA741696 Gov of Canada Gov of Canada 1 0.94238   0.09347   0.76404   0.51048   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48979 48979 SRR7535437 SRX4403221 SRS3557710 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample33 F3LFL4   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3LFL4 L33 F3LFL4 L33 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3LFL4.fastq.gz fastq 3167171318.0 37581804.0 F3LFL4.fastq.gz 0:84.27 1:0 A:836474638;C:736638892;G:687417511;T:906580806;N:59471 84 0     836474638 736638892 687417511 906580806 59471 SRX4403221 SRS3557710 SRA741696 Gov of Canada Gov of Canada 1 0.95381   0.0776   0.74432   0.49786   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48980 48980 SRR7535438 SRX4403220 SRS3557709 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample32 F3LFL3   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3LFL3 L32 F3LFL3 L32 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3LFL3.fastq.gz fastq 3969872568.0 47103172.0 F3LFL3.fastq.gz 0:84.28 1:0 A:1087899347;C:891968649;G:846315646;T:1143611603;N:77323 84 0     1087899347 891968649 846315646 1143611603 77323 SRX4403220 SRS3557709 SRA741696 Gov of Canada Gov of Canada 1 0.94717   0.08461   0.74714   0.53355   84   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48981 48981 SRR7535439 SRX4403219 SRS3557708 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample31 F3LFL2   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3LFL2 L31 F3LFL2 L31 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3LFL2.fastq.gz fastq 2401613544.0 31959346.0 F3LFL2.fastq.gz 0:75.15 1:0 A:673230842;C:536445759;G:492980009;T:698882870;N:74064 75 0     673230842 536445759 492980009 698882870 74064 SRX4403219 SRS3557708 SRA741696 Gov of Canada Gov of Canada 1 0.95198   0.08486   0.7878   0.55398   75   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48982 48982 SRR7535440 SRX4403218 SRS3557706 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample40 F3HFL3   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3HFL3 L40 F3HFL3 L40 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3HFL3.fastq.gz fastq 2266960447.0 26913177.0 F3HFL3.fastq.gz 0:84.23 1:0 A:590021990;C:520283209;G:479594101;T:677024566;N:36581 84 0     590021990 520283209 479594101 677024566 36581 SRX4403218 SRS3557706 SRA741696 Gov of Canada Gov of Canada 1 0.94897   0.08251   0.80848   0.57355   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
48983 48983 SRR7535441 SRX4403217 SRS3557707 SRP154295 PRJNA481502 Transgenerational hypocortisolism and behavioral disruption is induced by the antidepressant fluoxetine in male zebrafish Danio rerio PRJNA481502 Transcriptome Analysis Transcriptomic profiling of the whole kidney revealed that early fluoxetine exposure significantly transgenerationally modified numerous pathways closely associated with cortisol synthesis in the male adults from the F0 and F3 generations.   pubmed:30530669   sample39 F3HFL2   strain:AB strain|age:6 mpf organism or animal                 RNA seq of Danio rerio: male kidney F3HFL2 L39 F3HFL2 L39 mRNA seq from total RNA on Illumina Neoprep     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   SRP154295     F3HFL2.fastq.gz fastq 2749128323.0 32649931.0 F3HFL2.fastq.gz 0:84.20 1:0 A:739282939;C:602311637;G:590565979;T:816929591;N:38177 84 0     739282939 602311637 590565979 816929591 38177 SRX4403217 SRS3557707 SRA741696 Gov of Canada Gov of Canada 1 0.9613   0.09046   0.8104   0.62158   85   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Canada 2018-12-11 Adult Adult Kidney Renal System
49049 49049 SRR7633485 SRX4497216 SRS3618216 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 pod 03 GSM3317057   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G2 mRNA G2 pod 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G2 mRNA GSM3317057 GSM3317057: G2 pod 03; Danio rerio; RNA Seq GSM3317057   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317057 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S9_trimmed.fastq.gz fastq 1265733350.0 25073196.0 GSM3317057 r1 0:50.48 1:0 A:351449147;C:285891495;G:278677300;T:349486454;N:228954 50 0     351449147 285891495 278677300 349486454 228954 SRX4497216 SRS3618216 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.88664   0.09978   0.70747   0.46307   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49050 49050 SRR7633484 SRX4497215 SRS3618215 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 pod 02 GSM3317056   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G2 mRNA G2 pod 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G2 mRNA GSM3317056 GSM3317056: G2 pod 02; Danio rerio; RNA Seq GSM3317056   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317056 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S8_trimmed.fastq.gz fastq 927703036.0 18397661.0 GSM3317056 r1 0:50.43 1:0 A:256098583;C:212027468;G:205646180;T:253765375;N:165430 50 0     256098583 212027468 205646180 253765375 165430 SRX4497215 SRS3618215 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.82269   0.09332   0.70676   0.47673   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49051 49051 SRR7633483 SRX4497214 SRS3618214 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 pod 01 GSM3317055   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G2 mRNA G2 pod 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G2 mRNA GSM3317055 GSM3317055: G2 pod 01; Danio rerio; RNA Seq GSM3317055   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317055 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S7_trimmed.fastq.gz fastq 1868917850.0 36965227.0 GSM3317055 r1 0:50.56 1:0 A:518334465;C:423085551;G:412301170;T:514857394;N:339270 50 0     518334465 423085551 412301170 514857394 339270 SRX4497214 SRS3618214 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.8967   0.11444   0.66793   0.47524   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49052 49052 SRR7633482 SRX4497213 SRS3618213 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 pod 03 GSM3317054   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G0 mRNA G0 pod 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G0 mRNA GSM3317054 GSM3317054: G0 pod 03; Danio rerio; RNA Seq GSM3317054   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317054 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S6_trimmed.fastq.gz fastq 1989842108.0 39354652.0 GSM3317054 r1 0:50.56 1:0 A:547820589;C:452831323;G:441782569;T:547047192;N:360435 50 0     547820589 452831323 441782569 547047192 360435 SRX4497213 SRS3618213 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.88797   0.1001   0.67016   0.46755   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49053 49053 SRR7633481 SRX4497212 SRS3618212 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 pod 02 GSM3317053   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G0 mRNA G0 pod 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G0 mRNA GSM3317053 GSM3317053: G0 pod 02; Danio rerio; RNA Seq GSM3317053   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317053 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S5_trimmed.fastq.gz fastq 1784099065.0 35295758.0 GSM3317053 r1 0:50.55 1:0 A:493338451;C:401706697;G:388876128;T:499853218;N:324571 50 0     493338451 401706697 388876128 499853218 324571 SRX4497212 SRS3618212 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.86757   0.09319   0.6733   0.46511   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49054 49054 SRR7633480 SRX4497211 SRS3618211 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 pod 01 GSM3317052   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G0 mRNA G0 pod 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G0 mRNA GSM3317052 GSM3317052: G0 pod 01; Danio rerio; RNA Seq GSM3317052   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317052 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S4_trimmed.fastq.gz fastq 1294942611.0 25649695.0 GSM3317052 r1 0:50.49 1:0 A:358939215;C:292943376;G:284204779;T:358621256;N:233985 50 0     358939215 292943376 284204779 358621256 233985 SRX4497211 SRS3618211 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89677   0.09742   0.66695   0.46036   49   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49055 49055 SRR7633479 SRX4497210 SRS3618210 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control pod 03 GSM3317051   tissue:zebrafish podocyte|line:pod:mCherry|treatment:control control pod 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:control GSM3317051 GSM3317051: control pod 03; Danio rerio; RNA Seq GSM3317051   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317051 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S3_trimmed.fastq.gz fastq 1864996530.0 36896407.0 GSM3317051 r1 0:50.55 1:0 A:514542102;C:423583183;G:412707586;T:513826127;N:337532 50 0     514542102 423583183 412707586 513826127 337532 SRX4497210 SRS3618210 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89167   0.10091   0.67773   0.48093   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49056 49056 SRR7633478 SRX4497209 SRS3618209 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control pod 02 GSM3317050   tissue:zebrafish podocyte|line:pod:mCherry|treatment:control control pod 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:control GSM3317050 GSM3317050: control pod 02; Danio rerio; RNA Seq GSM3317050   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317050 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S2_trimmed.fastq.gz fastq 1405360276.0 27811908.0 GSM3317050 r1 0:50.53 1:0 A:388467227;C:319138771;G:310773160;T:386727396;N:253722 50 0     388467227 319138771 310773160 386727396 253722 SRX4497209 SRS3618209 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.898   0.10269   0.66967   0.45546   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49057 49057 SRR7633477 SRX4497208 SRS3618208 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control pod 01 GSM3317049   tissue:zebrafish podocyte|line:pod:mCherry|treatment:control control pod 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:control GSM3317049 GSM3317049: control pod 01; Danio rerio; RNA Seq GSM3317049   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317049 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S1_trimmed.fastq.gz fastq 931525657.0 18454172.0 GSM3317049 r1 0:50.48 1:0 A:259125695;C:210068089;G:204402139;T:257763012;N:166722 50 0     259125695 210068089 204402139 257763012 166722 SRX4497208 SRS3618208 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89072   0.10423   0.67107   0.46057   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
51852 51852 SRR10358701 SRX7068102 SRS5584514 SRP192333 PRJNA532380 Danio rerio SVCV infection PRJNA532380 Other Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.       Model organism or animal sample from Danio rerio miRNA WT SVCV   strain:Wild type|age:6 month|sex:pooled male and female|tissue:kidney|BioSampleModel:Model organism or animal                 miRNA WT SVCV miRNA WT SVCV miRNA WT SVCV Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.     miRNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP192333     WT-SVCV_1.fastq.gz fastq 1316699181.0 25817631.0 WT SVCV 1.fastq.gz 0:51 A:276414308;C:338128957;G:380963712;T:321185951;N:6253 51       276414308 338128957 380963712 321185951 6253 SRX7068102 SRS5584514 SRA986546 IIM - CSIC|Biotechnology and Aquaculture IIM - CSIC 1 0.12679   0.0134   0.9931   0.63608   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2019-10-29 Adult Adult Kidney Renal System
51853 51853 SRR10358540 SRX7067941 SRS5584353 SRP192333 PRJNA532380 Danio rerio SVCV infection PRJNA532380 Other Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.       Model organism or animal sample from Danio rerio miRNA WT Control   strain:Wild type|age:6 month|sex:pooled male and female|tissue:kidney|BioSampleModel:Model organism or animal                 miRNA WT Control miRNA WT Control miRNA WT Control Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.     miRNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP192333     WT-C_1.fastq.gz fastq 1391330184.0 27280984.0 WT C 1.fastq.gz 0:51 A:252097427;C:365291036;G:426841004;T:347094254;N:6463 51       252097427 365291036 426841004 347094254 6463 SRX7067941 SRS5584353 SRA986495 IIM - CSIC|Biotechnology and Aquaculture IIM - CSIC 1 0.01783   0.00242   0.99411   0.61368   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2019-10-29 Adult Adult Kidney Renal System
60502 60502 SRR12338629 SRX8838545 SRS7101853 SRP273930 PRJNA649208 A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation GSE155258 Transcriptome Analysis Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …       AMut3 S16 GSM4698247   source name:grna / mutant fish|tissue:kidney marrow|genotype:grna / AMut3 S16 RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample. grna / mutant fish Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines. tissue:kidney marrow|genotype:grna / GSM4698247 GSM4698247: AMut3 S16; Danio rerio; RNA Seq GSM4698247   1 Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. GEO Accession:GSM4698247 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP273930     AMut3_S16_L003_R1_001.fastq.gz fastq 1660975744.0 21854944.0 GSM4698247 r1 0:76 1:0 A:403133854;C:408666497;G:390547168;T:458402036;N:226189 76 0     403133854 408666497 390547168 458402036 226189 SRX8838545 SRS7101853 SRA1104643 GEO Boolean, Pediatrics, UCSD 1 0.88856   0.071   0.7331   0.50274   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-07-28 Undetermined Undetermined Kidney Renal System
60503 60503 SRR12338628 SRX8838544 SRS7101852 SRP273930 PRJNA649208 A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation GSE155258 Transcriptome Analysis Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …       AMut2 S15 GSM4698246   source name:grna / mutant fish|tissue:kidney marrow|genotype:grna / AMut2 S15 RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample. grna / mutant fish Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines. tissue:kidney marrow|genotype:grna / GSM4698246 GSM4698246: AMut2 S15; Danio rerio; RNA Seq GSM4698246   1 Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. GEO Accession:GSM4698246 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP273930     AMut2_S15_L003_R1_001.fastq.gz fastq 1932204620.0 25423745.0 GSM4698246 r1 0:76 1:0 A:471753150;C:472824626;G:455434892;T:531926834;N:265118 76 0     471753150 472824626 455434892 531926834 265118 SRX8838544 SRS7101852 SRA1104643 GEO Boolean, Pediatrics, UCSD 1 0.88563   0.0647   0.73054   0.51301   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-07-28 Undetermined Undetermined Kidney Renal System
60504 60504 SRR12338627 SRX8838543 SRS7101851 SRP273930 PRJNA649208 A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation GSE155258 Transcriptome Analysis Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …       AMut1 S14 GSM4698245   source name:grna / mutant fish|tissue:kidney marrow|genotype:grna / AMut1 S14 RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample. grna / mutant fish Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines. tissue:kidney marrow|genotype:grna / GSM4698245 GSM4698245: AMut1 S14; Danio rerio; RNA Seq GSM4698245   1 Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. GEO Accession:GSM4698245 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP273930     AMut1_S14_L003_R1_001.fastq.gz fastq 1576218644.0 20739719.0 GSM4698245 r1 0:76 1:0 A:382135276;C:389342906;G:367829537;T:436699819;N:211106 76 0     382135276 389342906 367829537 436699819 211106 SRX8838543 SRS7101851 SRA1104643 GEO Boolean, Pediatrics, UCSD 1 0.88823   0.07406   0.73062   0.50537   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-07-28 Undetermined Undetermined Kidney Renal System
60505 60505 SRR12338626 SRX8838542 SRS7101850 SRP273930 PRJNA649208 A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation GSE155258 Transcriptome Analysis Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …       WT3 S13 GSM4698244   source name:grna+/+ control fish|tissue:kidney marrow|genotype:WT WT3 S13 RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample. grna+/+ control fish Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines. tissue:kidney marrow|genotype:WT GSM4698244 GSM4698244: WT3 S13; Danio rerio; RNA Seq GSM4698244   1 Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. GEO Accession:GSM4698244 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP273930     WT3_S13_L003_R1_001.fastq.gz fastq 1763410824.0 23202774.0 GSM4698244 r1 0:76 1:0 A:423301555;C:439721210;G:408339976;T:491805474;N:242609 76 0     423301555 439721210 408339976 491805474 242609 SRX8838542 SRS7101850 SRA1104643 GEO Boolean, Pediatrics, UCSD 1 0.89892   0.06886   0.74408   0.49795   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-07-28 Undetermined Undetermined Kidney Renal System
60506 60506 SRR12338625 SRX8838541 SRS7101849 SRP273930 PRJNA649208 A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation GSE155258 Transcriptome Analysis Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …       WT2 S12 GSM4698243   source name:grna+/+ control fish|tissue:kidney marrow|genotype:WT WT2 S12 RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample. grna+/+ control fish Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines. tissue:kidney marrow|genotype:WT GSM4698243 GSM4698243: WT2 S12; Danio rerio; RNA Seq GSM4698243   1 Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. GEO Accession:GSM4698243 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP273930     WT2_S12_L003_R1_001.fastq.gz fastq 1637691700.0 21548575.0 GSM4698243 r1 0:76 1:0 A:405974612;C:400305204;G:377359541;T:453830617;N:221726 76 0     405974612 400305204 377359541 453830617 221726 SRX8838541 SRS7101849 SRA1104643 GEO Boolean, Pediatrics, UCSD 1 0.89995   0.07959   0.7429   0.5021   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-07-28 Undetermined Undetermined Kidney Renal System
60507 60507 SRR12338624 SRX8838540 SRS7101848 SRP273930 PRJNA649208 A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation GSE155258 Transcriptome Analysis Granulin GRN is a pleiotropic protein involved in inflammation wound healing neurodegenerative disease and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis frontotemporal dementia and to enhance wound healing. How granulin contributes to each of these diverse biological functions however remains largely unknown. Here we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a grna and fail to express the myeloid genes cebpa rgs2 lyz mpx mpeg1 mfap4 and apoeb. Pathology studies in combination with RNA sequencing show that in addition to facilitating myeloid cell differentiation granulin actively inhibits the erythroid program. Moreover grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically we have performed CUT&RUN for the first time in zebrafish and identified that Pu.1 directly binds grna enhancers triggering its expression. Similarly mammalian granulin is also upregulated in myeloid cells and its expression is controlled by the myeloid transcription factors PU.1 and IRF8 demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation opening a new field of study that will help elucidate how granulin impacts inflammation wound healing tumor progression and neurodegenerative disease. Overall design: Adult grna / and grna+/+ control fish three fish per condition were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy Qiagen following …       WT1 S11 GSM4698242   source name:grna+/+ control fish|tissue:kidney marrow|genotype:WT WT1 S11 RNASeq data was mapped to Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 using Olego Wu Anczukow et al. 2013 featureCounts Liao Smyth et al. 2014 from subread package is used to compute the raw read counts for each gene. TPM Transcripts Per MillionsLi & Dewey 2011 Pachter 2011 values were computed from the raw read counts using a custom perl script and log2TPM+1 is used to compute the final log reduced expression values. DESeq2 1.26.0 Love Huber et al. 2014 R package is used to compute differentially expressed genes at 1% false discovery rate. Genome build: Reference Consortium Zebrafish Build 10 UCSC Genome GRCz10/danRer10; Sept 2014 Supplementary files format and content: tab delimited text files include TPM values for each Sample. grna+/+ control fish Six kidney marrows were used to perform RNA seq. One kidney marrow per sample. Triplicates were used per sample: three grna+/+ and three grna / siblings Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer’s instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. Zebrafish Danio rerio were raised as described Westerfield 2000 in a circulating aquarium system Aquaneering at 28°C and maintained in accordance with ISU and UCSD IACUC guidelines. tissue:kidney marrow|genotype:WT GSM4698242 GSM4698242: WT1 S11; Danio rerio; RNA Seq GSM4698242   1 Zebrafish grna / and grna+/+ control siblings were anesthetized in tricaine subjected to cardiocentesis and kidney dissection as previously described Traver et al. 2003. The resulting kidney suspension was gently triturated with a P1000 pipette and filtered with a 30µm cell strainer. The cell suspension was lysated in RLT buffer and total RNA extraceted using RNeasy Qiagen following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200 and samples with an RNA Integrity Number RIN greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Illumina San Diego CA. Samples were processed following manufacturer's instructions starting with 50 ng of RNA and modifying RNA shear time to five minutes. GEO Accession:GSM4698242 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP273930     WT1_S11_L003_R1_001.fastq.gz fastq 1817974948.0 23920723.0 GSM4698242 r1 0:76 1:0 A:445440119;C:445993982;G:423050638;T:503235344;N:254865 76 0     445440119 445993982 423050638 503235344 254865 SRX8838540 SRS7101848 SRA1104643 GEO Boolean, Pediatrics, UCSD 1 0.89811   0.07554   0.72908   0.4892   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2020-07-28 Undetermined Undetermined Kidney Renal System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;