{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", technology = \"bulk\" and tissue_curation = \"Kidney\"", "rows": [[33653, "SRR30355362", "SRX25813460", "SRS22443728", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "Rad21het rep3", "GSM8479116", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep3", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479116", "GSM8479116: Rad21het rep3; Danio rerio; RNA Seq", "GSM8479116 r1", "GSM8479116", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. 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Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "Rad21het rep2", "GSM8479115", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep2", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479115", "GSM8479115: Rad21het rep2; Danio rerio; RNA Seq", "GSM8479115 r1", "GSM8479115", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "Rad21het_rep2_L001_R1_001.fastq.gz Rad21het_rep2_L001_R2_001.fastq.gz", "fastq fastq", 15263700610.0, 50542055.0, "GSM8479115 r1", "0:151 1:151", "A:3934169632;C:3701506984;G:3857649812;T:3769115522;N:1258660", 151, 151, null, null, 3934169632, 3701506984, 3857649812, 3769115522, 1258660, "SRX25813459", "SRS22443727", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.9227, 0.92195, 0.02689, 0.02669, 0.72547, 0.73196, 0.47904, 0.48582, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33655, "SRR30355364", "SRX25813458", "SRS22443726", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "Rad21het rep1", "GSM8479114", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep1", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479114", "GSM8479114: Rad21het rep1; Danio rerio; RNA Seq", "GSM8479114 r1", "GSM8479114", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "Rad21het_rep1_L001_R1_001.fastq.gz Rad21het_rep1_L001_R2_001.fastq.gz", "fastq fastq", 12383733782.0, 41005741.0, "GSM8479114 r1", "0:151 1:151", "A:3185412651;C:3011130011;G:3135728222;T:3050446997;N:1015901", 151, 151, null, null, 3185412651, 3011130011, 3135728222, 3050446997, 1015901, "SRX25813458", "SRS22443726", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.9242, 0.92383, 0.0273, 0.02728, 0.72151, 0.72683, 0.47619, 0.48803, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33656, "SRR30355365", "SRX25813457", "SRS22443744", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "WT rep3", "GSM8479113", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep3", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479113", "GSM8479113: WT rep3; Danio rerio; RNA Seq", "GSM8479113 r1", "GSM8479113", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "WT_rep3_L001_R1_001.fastq.gz WT_rep3_L001_R2_001.fastq.gz", "fastq fastq", 13242216498.0, 43848399.0, "GSM8479113 r1", "0:151 1:151", "A:3400902046;C:3224156106;G:3363313174;T:3252754642;N:1090530", 151, 151, null, null, 3400902046, 3224156106, 3363313174, 3252754642, 1090530, "SRX25813457", "SRS22443744", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.91607, 0.91443, 0.02817, 0.02789, 0.705, 0.7107, 0.51363, 0.49767, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33657, "SRR30355366", "SRX25813456", "SRS22443725", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "WT rep2", "GSM8479112", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep2", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479112", "GSM8479112: WT rep2; Danio rerio; RNA Seq", "GSM8479112 r1", "GSM8479112", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "WT_rep2_L001_R1_001.fastq.gz WT_rep2_L001_R2_001.fastq.gz", "fastq fastq", 10248296614.0, 33934757.0, "GSM8479112 r1", "0:151 1:151", "A:2636593190;C:2486812997;G:2585808493;T:2538244274;N:837660", 151, 151, null, null, 2636593190, 2486812997, 2585808493, 2538244274, 837660, "SRX25813456", "SRS22443725", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.91112, 0.91075, 0.02202, 0.02161, 0.70942, 0.71719, 0.47568, 0.49773, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33658, "SRR30355367", "SRX25813455", "SRS22443724", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "WT rep1", "GSM8479111", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep1", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479111", "GSM8479111: WT rep1; Danio rerio; RNA Seq", "GSM8479111 r1", "GSM8479111", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "WT_rep1_L001_R1_001.fastq.gz WT_rep1_L001_R2_001.fastq.gz", "fastq fastq", 11368938584.0, 37645492.0, "GSM8479111 r1", "0:151 1:151", "A:2896983545;C:2796736516;G:2916252779;T:2758034822;N:930922", 151, 151, null, null, 2896983545, 2796736516, 2916252779, 2758034822, 930922, "SRX25813455", "SRS22443724", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.91882, 0.91785, 0.02974, 0.02968, 0.72105, 0.72693, 0.50274, 0.49954, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [42615, "SRR5810949", "SRX2989499", "SRS2341423", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "IL2RGA rep3 bulkRNA", "GSM2696362", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:IL2RGA", "IL2RGA rep3 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:IL2RGA", "GSM2696362", "GSM2696362: IL2RGA rep3 bulkRNA; Danio rerio; RNA Seq", "GSM2696362", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696362", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "IL2RGA_rep3.bam", "bam", 800560362.0, 7848631.0, "GSM2696362 r1", "0:51 1:51", "A:204943188;C:193859822;G:198825795;T:202880780;N:50777", 51, 51, null, null, 204943188, 193859822, 198825795, 202880780, 50777, "SRX2989499", "SRS2341423", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.9537, 0.95854, 0.14459, 0.14217, 0.72297, 0.72165, 0.53136, 0.5294, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42616, "SRR5810948", "SRX2989498", "SRS2341422", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "IL2RGA rep2 bulkRNA", "GSM2696361", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:IL2RGA", "IL2RGA rep2 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:IL2RGA", "GSM2696361", "GSM2696361: IL2RGA rep2 bulkRNA; Danio rerio; RNA Seq", "GSM2696361", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696361", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "IL2RGA_rep2.bam", "bam", 1103288814.0, 10816557.0, "GSM2696361 r1", "0:51 1:51", "A:296109551;C:253391201;G:259742934;T:293977435;N:67693", 51, 51, null, null, 296109551, 253391201, 259742934, 293977435, 67693, "SRX2989498", "SRS2341422", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.93568, 0.946, 0.07751, 0.07604, 0.67568, 0.67616, 0.49311, 0.49081, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42617, "SRR5810947", "SRX2989497", "SRS2341420", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "IL2RGA rep1 bulkRNA", "GSM2696360", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:IL2RGA", "IL2RGA rep1 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:IL2RGA", "GSM2696360", "GSM2696360: IL2RGA rep1 bulkRNA; Danio rerio; RNA Seq", "GSM2696360", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696360", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "IL2RGA_rep1.bam", "bam", 661646358.0, 6486729.0, "GSM2696360 r1", "0:51 1:51", "A:169428837;C:164616195;G:161161362;T:166407987;N:31977", 51, 51, null, null, 169428837, 164616195, 161161362, 166407987, 31977, "SRX2989497", "SRS2341420", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.91331, 0.93442, 0.06212, 0.06166, 0.69915, 0.69964, 0.4776, 0.5104, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42618, "SRR5810946", "SRX2989496", "SRS2341419", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "PRKDC.IL2RGA rep3 bulkRNA", "GSM2696359", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC;IL2RGA", "PRKDC.IL2RGA rep3 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:PRKDC;IL2RGA", "GSM2696359", "GSM2696359: PRKDC.IL2RGA rep3 bulkRNA; Danio rerio; RNA Seq", "GSM2696359", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696359", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "PRKDC.IL2RGA_rep3.bam", "bam", 887363484.0, 8699642.0, "GSM2696359 r1", "0:51 1:51", "A:236785705;C:205238782;G:210240418;T:235045073;N:53506", 51, 51, null, null, 236785705, 205238782, 210240418, 235045073, 53506, "SRX2989496", "SRS2341419", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.92505, 0.93893, 0.07173, 0.07011, 0.71461, 0.71435, 0.48699, 0.49848, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42619, "SRR5810945", "SRX2989495", "SRS2341417", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "PRKDC.IL2RGA rep2 bulkRNA", "GSM2696358", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC;IL2RGA", "PRKDC.IL2RGA rep2 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:PRKDC;IL2RGA", "GSM2696358", "GSM2696358: PRKDC.IL2RGA rep2 bulkRNA; Danio rerio; RNA Seq", "GSM2696358", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "PRKDC.IL2RGA_rep2.bam", "bam", 1243263312.0, 12188856.0, "GSM2696358 r1", "0:51 1:51", "A:335332471;C:284322063;G:289732846;T:333799129;N:76803", 51, 51, null, null, 335332471, 284322063, 289732846, 333799129, 76803, "SRX2989495", "SRS2341417", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.93625, 0.94489, 0.08706, 0.08568, 0.68956, 0.69067, 0.49006, 0.48855, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42620, "SRR5810944", "SRX2989494", "SRS2341418", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "PRKDC.IL2RGA rep1 bulkRNA", "GSM2696357", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC;IL2RGA", "PRKDC.IL2RGA rep1 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:PRKDC;IL2RGA", "GSM2696357", "GSM2696357: PRKDC.IL2RGA rep1 bulkRNA; Danio rerio; RNA Seq", "GSM2696357", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696357", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "PRKDC.IL2RGA_rep1.bam", "bam", 1186402800.0, 11631400.0, "GSM2696357 r1", "0:51 1:51", "A:318338106;C:272405192;G:278795626;T:316790310;N:73566", 51, 51, null, null, 318338106, 272405192, 278795626, 316790310, 73566, "SRX2989494", "SRS2341418", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.93146, 0.94427, 0.06375, 0.0617, 0.69664, 0.69566, 0.48745, 0.47922, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42621, "SRR5810943", "SRX2989493", "SRS2341416", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "PRKDC rep3 bulkRNA", "GSM2696356", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC", "PRKDC rep3 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:PRKDC", "GSM2696356", "GSM2696356: PRKDC rep3 bulkRNA; Danio rerio; RNA Seq", "GSM2696356", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696356", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "PRKDC_rep3.bam", "bam", 1086096306.0, 10648003.0, "GSM2696356 r1", "0:51 1:51", "A:290117045;C:250914550;G:254803671;T:289025322;N:1235718", 51, 51, null, null, 290117045, 250914550, 254803671, 289025322, 1235718, "SRX2989493", "SRS2341416", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.93491, 0.92916, 0.13346, 0.12712, 0.69974, 0.69996, 0.49518, 0.48499, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42622, "SRR5810942", "SRX2989492", "SRS2341415", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "PRKDC rep2 bulkRNA", "GSM2696355", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC", "PRKDC rep2 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:PRKDC", "GSM2696355", "GSM2696355: PRKDC rep2 bulkRNA; Danio rerio; RNA Seq", "GSM2696355", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696355", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "PRKDC_rep2.bam", "bam", 1295111136.0, 12697168.0, "GSM2696355 r1", "0:51 1:51", "A:347365385;C:295754109;G:304296998;T:346181142;N:1513502", 51, 51, null, null, 347365385, 295754109, 304296998, 346181142, 1513502, "SRX2989492", "SRS2341415", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.93286, 0.923, 0.13571, 0.1291, 0.70512, 0.70796, 0.49872, 0.49014, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42623, "SRR5810941", "SRX2989491", "SRS2341414", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "PRKDC rep1 bulkRNA", "GSM2696354", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:PRKDC", "PRKDC rep1 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:PRKDC", "GSM2696354", "GSM2696354: PRKDC rep1 bulkRNA; Danio rerio; RNA Seq", "GSM2696354", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696354", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "PRKDC_rep1.bam", "bam", 1144774866.0, 11223283.0, "GSM2696354 r1", "0:51 1:51", "A:307919037;C:260831758;G:268914919;T:305733316;N:1375836", 51, 51, null, null, 307919037, 260831758, 268914919, 305733316, 1375836, "SRX2989491", "SRS2341414", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.93261, 0.92672, 0.12175, 0.11566, 0.704, 0.70597, 0.49649, 0.49333, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42624, "SRR5810940", "SRX2989490", "SRS2341413", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "WT rep3 bulkRNA", "GSM2696353", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:wildtype", "WT rep3 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:wildtype", "GSM2696353", "GSM2696353: WT rep3 bulkRNA; Danio rerio; RNA Seq", "GSM2696353", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696353", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "WT_rep3.bam", "bam", 1222568532.0, 11985966.0, "GSM2696353 r1", "0:51 1:51", "A:325706008;C:281709574;G:290313610;T:323399233;N:1440107", 51, 51, null, null, 325706008, 281709574, 290313610, 323399233, 1440107, "SRX2989490", "SRS2341413", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.92438, 0.92382, 0.11926, 0.11474, 0.69934, 0.70116, 0.50348, 0.50642, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42625, "SRR5810939", "SRX2989489", "SRS2341412", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "WT rep2 bulkRNA", "GSM2696352", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:wildtype", "WT rep2 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:wildtype", "GSM2696352", "GSM2696352: WT rep2 bulkRNA; Danio rerio; RNA Seq", "GSM2696352", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696352", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "WT_rep2.bam", "bam", 1169509356.0, 11465778.0, "GSM2696352 r1", "0:51 1:51", "A:311703416;C:268894082;G:278866430;T:308727612;N:1317816", 51, 51, null, null, 311703416, 268894082, 278866430, 308727612, 1317816, "SRX2989489", "SRS2341412", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.91371, 0.92007, 0.1137, 0.10922, 0.70735, 0.7093, 0.49742, 0.49982, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [42626, "SRR5810938", "SRX2989488", "SRS2341411", "SRP111341", "PRJNA393430", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA seq]", "GSE100912", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "WT rep1 bulkRNA", "GSM2696351", null, "source name:whole kidney marrow|tissue:kidney marrow|genotype:wildtype", "WT rep1 bulkRNA", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", null, "tissue:kidney marrow|genotype:wildtype", "GSM2696351", "GSM2696351: WT rep1 bulkRNA; Danio rerio; RNA Seq", "GSM2696351", null, "1", "Wild type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 \u00b5l of QIAGEN RLT buffer containing 1% 2 Mercaptoethanol  followed by RNA isolation using the RNAeasy Mini kit QIAGEN. 100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext\u00ae PolyA mRNA Magnetic Isolation Module  followed by NGS library construction using NEBNext\u00ae Ultra\u2122 Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike in.", "GEO Accession:GSM2696351", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP111341", null, null, "WT_rep1.bam", "bam", 1371866442.0, 13449671.0, "GSM2696351 r1", "0:51 1:51", "A:360833799;C:320009757;G:330603707;T:358760329;N:1658850", 51, 51, null, null, 360833799, 320009757, 330603707, 358760329, 1658850, "SRX2989488", "SRS2341411", "SRA584590", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.94532, 0.93582, 0.11053, 0.10605, 0.70686, 0.70869, 0.48301, 0.4993, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "sc", "bulk", "bulk", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"], [49485, "SRR7909922", "SRX4746039", "SRS3826039", "SRP162761", "PRJNA493632", "Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [Bulk RNA seq]", "GSE120578", "Transcriptome Analysis", "To characterize the distinct features of HSPCs and relevant niche cells  we performed RNA seq with sorted zebrafish HSPCs and niche cells  based on fluorescent protein labeling from distinct regions at six relatively discrete stages. Overall design: We used double transgenic line Tg kdrl:mCherry/CD41:GFP and sorted HSCs  ECs and NCs from embryonic tails at 36 hpf  52 hpf  3 dpf and 4 dpf. And we sorted HSPCs and NCs from CD41: GFP kidney marrow at 3 mpf.", "parent bioproject:PRJNA493631", "pubmed:31042481;pubmed:33785593", null, "3 mpf kidney NC rep2", "GSM3403661", null, "source name:zebrafish embryos|tissue:zebrafish kidney|cell type:double negative cells|Stage:3 mpf", "3 mpf kidney NC rep2", "Reads quality were first checked by \"Fastqc\" And then clean reads were mapped to the reference genome by HISAT Uniquely mapped reads were utilized to calculate the counts of each gene by HTSeq Reads counts matrix was then normalized to library size by DESeq2 with default parameters  and normalized reads were then used to calculate the FPKM Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples  measured by FPKM", "zebrafish embryos", null, "The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.", null, "tissue:zebrafish kidney|cell type:double negative cells|Stage:3 mpf", "GSM3403661", "GSM3403661: 3 mpf kidney NC rep2; Danio rerio; RNA Seq", "GSM3403661", null, "1", "The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.", "GEO Accession:GSM3403661", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP162761", null, null, "KM-NC-2_HNF2MCCXX_L8_2.clean.fq.gz KM-NC-2_HNF2MCCXX_L8_1.clean.fq.gz", "fastq fastq", 7885023900.0, 26283413.0, "GSM3403661 r1", "0:150 1:150", "A:2133473243;C:1787053126;G:1830087423;T:2133420067;N:990041", 150, 150, null, null, 2133473243, 1787053126, 1830087423, 2133420067, 990041, "SRX4746039", "SRS3826039", "SRA785160", "GEO", "Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)", 2, 0.6537, 0.65202, 0.23748, 0.23535, 0.70337, 0.70962, 0.50508, 0.50701, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2018-09-27", "Adult", "Adult", "Kidney", "Renal System"], [49486, "SRR7909921", "SRX4746038", "SRS3826038", "SRP162761", "PRJNA493632", "Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [Bulk RNA seq]", "GSE120578", "Transcriptome Analysis", "To characterize the distinct features of HSPCs and relevant niche cells  we performed RNA seq with sorted zebrafish HSPCs and niche cells  based on fluorescent protein labeling from distinct regions at six relatively discrete stages. Overall design: We used double transgenic line Tg kdrl:mCherry/CD41:GFP and sorted HSCs  ECs and NCs from embryonic tails at 36 hpf  52 hpf  3 dpf and 4 dpf. And we sorted HSPCs and NCs from CD41: GFP kidney marrow at 3 mpf.", "parent bioproject:PRJNA493631", "pubmed:31042481;pubmed:33785593", null, "3 mpf kidney NC rep1", "GSM3403660", null, "source name:zebrafish embryos|tissue:zebrafish kidney|cell type:double negative cells|Stage:3 mpf", "3 mpf kidney NC rep1", "Reads quality were first checked by \"Fastqc\" And then clean reads were mapped to the reference genome by HISAT Uniquely mapped reads were utilized to calculate the counts of each gene by HTSeq Reads counts matrix was then normalized to library size by DESeq2 with default parameters  and normalized reads were then used to calculate the FPKM Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples  measured by FPKM", "zebrafish embryos", null, "The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.", null, "tissue:zebrafish kidney|cell type:double negative cells|Stage:3 mpf", "GSM3403660", "GSM3403660: 3 mpf kidney NC rep1; Danio rerio; RNA Seq", "GSM3403660", null, "1", "The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.", "GEO Accession:GSM3403660", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP162761", null, null, "KM-3m-NC-1_HVLMNCCXX_L3_1.clean.fq.gz KM-3m-NC-1_HVLMNCCXX_L3_2.clean.fq.gz", "fastq fastq", 8651865300.0, 28839551.0, "GSM3403660 r1", "0:150 1:150", "A:2162011423;C:2147099803;G:2180299523;T:2161654484;N:800067", 150, 150, null, null, 2162011423, 2147099803, 2180299523, 2161654484, 800067, "SRX4746038", "SRS3826038", "SRA785160", "GEO", "Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)", 2, 0.85302, 0.85444, 0.15014, 0.1504, 0.75402, 0.75741, 0.57991, 0.58881, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2018-09-27", "Adult", "Adult", "Kidney", "Renal System"], [49487, "SRR7909920", "SRX4746037", "SRS3826035", "SRP162761", "PRJNA493632", "Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [Bulk RNA seq]", "GSE120578", "Transcriptome Analysis", "To characterize the distinct features of HSPCs and relevant niche cells  we performed RNA seq with sorted zebrafish HSPCs and niche cells  based on fluorescent protein labeling from distinct regions at six relatively discrete stages. Overall design: We used double transgenic line Tg kdrl:mCherry/CD41:GFP and sorted HSCs  ECs and NCs from embryonic tails at 36 hpf  52 hpf  3 dpf and 4 dpf. And we sorted HSPCs and NCs from CD41: GFP kidney marrow at 3 mpf.", "parent bioproject:PRJNA493631", "pubmed:31042481;pubmed:33785593", null, "3 mpf kidney HSPC rep2", "GSM3403659", null, "source name:zebrafish embryos|tissue:zebrafish kidney|cell type:hematopoietic stem and progenitor cells|Stage:3 mpf", "3 mpf kidney HSPC rep2", "Reads quality were first checked by \"Fastqc\" And then clean reads were mapped to the reference genome by HISAT Uniquely mapped reads were utilized to calculate the counts of each gene by HTSeq Reads counts matrix was then normalized to library size by DESeq2 with default parameters  and normalized reads were then used to calculate the FPKM Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples  measured by FPKM", "zebrafish embryos", null, "The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.", null, "tissue:zebrafish kidney|cell type:hematopoietic stem and progenitor cells|Stage:3 mpf", "GSM3403659", "GSM3403659: 3 mpf kidney HSPC rep2; Danio rerio; RNA Seq", "GSM3403659", null, "1", "The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.", "GEO Accession:GSM3403659", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP162761", null, null, "KM-HSC-2_HVL3KCCXX_L5_2.clean.fq.gz KM-HSC-2_HVL3KCCXX_L5_1.clean.fq.gz", "fastq fastq", 7500884100.0, 25002947.0, "GSM3403659 r1", "0:150 1:150", "A:1962768405;C:1776596404;G:1801382831;T:1959696769;N:439691", 150, 150, null, null, 1962768405, 1776596404, 1801382831, 1959696769, 439691, "SRX4746037", "SRS3826035", "SRA785160", "GEO", "Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)", 2, 0.86016, 0.86402, 0.07806, 0.07827, 0.64971, 0.65431, 0.49809, 0.49801, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2018-09-27", "Adult", "Adult", "Kidney", "Renal System"], [49488, "SRR7909919", "SRX4746036", "SRS3826033", "SRP162761", "PRJNA493632", "Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [Bulk RNA seq]", "GSE120578", "Transcriptome Analysis", "To characterize the distinct features of HSPCs and relevant niche cells  we performed RNA seq with sorted zebrafish HSPCs and niche cells  based on fluorescent protein labeling from distinct regions at six relatively discrete stages. Overall design: We used double transgenic line Tg kdrl:mCherry/CD41:GFP and sorted HSCs  ECs and NCs from embryonic tails at 36 hpf  52 hpf  3 dpf and 4 dpf. And we sorted HSPCs and NCs from CD41: GFP kidney marrow at 3 mpf.", "parent bioproject:PRJNA493631", "pubmed:31042481;pubmed:33785593", null, "3 mpf kidney HSPC rep1", "GSM3403658", null, "source name:zebrafish embryos|tissue:zebrafish kidney|cell type:hematopoietic stem and progenitor cells|Stage:3 mpf", "3 mpf kidney HSPC rep1", "Reads quality were first checked by \"Fastqc\" And then clean reads were mapped to the reference genome by HISAT Uniquely mapped reads were utilized to calculate the counts of each gene by HTSeq Reads counts matrix was then normalized to library size by DESeq2 with default parameters  and normalized reads were then used to calculate the FPKM Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples  measured by FPKM", "zebrafish embryos", null, "The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.", null, "tissue:zebrafish kidney|cell type:hematopoietic stem and progenitor cells|Stage:3 mpf", "GSM3403658", "GSM3403658: 3 mpf kidney HSPC rep1; Danio rerio; RNA Seq", "GSM3403658", null, "1", "The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.", "GEO Accession:GSM3403658", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP162761", null, null, "KM-3m-HSC-1_HNH5YCCXX_L1_2.clean.fq.gz KM-3m-HSC-1_HNH5YCCXX_L1_1.clean.fq.gz", "fastq fastq", 9753863400.0, 32512878.0, "GSM3403658 r1", "0:150 1:150", "A:2466551005;C:2391701683;G:2419931505;T:2473619296;N:2059911", 150, 150, null, null, 2466551005, 2391701683, 2419931505, 2473619296, 2059911, "SRX4746036", "SRS3826033", "SRA785160", "GEO", "Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)", 2, 0.92914, 0.92755, 0.06268, 0.06222, 0.70301, 0.70634, 0.49243, 0.48036, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2018-09-27", "Adult", "Adult", "Kidney", "Renal System"], [60916, "SRR12658664", "SRX9139722", "SRS7381388", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney3", "GSM4792207", null, "source name:adult kidney|strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "runx1 /  kidney3", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "GSM4792207", "GSM4792207: runx1 /  kidney3; Danio rerio; RNA Seq", "GSM4792207", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792207", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_null_6.1.cln.fq.gz runx1_del25_null_6.2.cln.fq.gz", "fastq fastq", 9833070492.0, 39020121.0, "GSM4792207 r1", "0:126 1:126", "A:2595482323;C:2237794410;G:2283114442;T:2716679317;N:0", 126, 126, null, null, 2595482323, 2237794410, 2283114442, 2716679317, 0, "SRX9139722", "SRS7381388", "SRA1126725", "GEO", "NHGRI", 2, 0.95072, 0.95176, 0.08254, 0.08278, 0.72565, 0.7265, 0.55513, 0.55433, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60917, "SRR12658663", "SRX9139721", "SRS7381387", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney2", "GSM4792206", null, "source name:adult kidney|strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "runx1 /  kidney2", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "GSM4792206", "GSM4792206: runx1 /  kidney2; Danio rerio; RNA Seq", "GSM4792206", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792206", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_null_5.1.cln.fq.gz runx1_del25_null_5.2.cln.fq.gz", "fastq fastq", 10411105572.0, 41313911.0, "GSM4792206 r1", "0:126 1:126", "A:2758731492;C:2362241256;G:2412281429;T:2877851395;N:0", 126, 126, null, null, 2758731492, 2362241256, 2412281429, 2877851395, 0, "SRX9139721", "SRS7381387", "SRA1126725", "GEO", "NHGRI", 2, 0.9462, 0.94718, 0.09575, 0.09572, 0.74282, 0.74391, 0.53729, 0.53866, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60918, "SRR12658662", "SRX9139720", "SRS7381386", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney1", "GSM4792205", null, "source name:adult kidney|strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "runx1 /  kidney1", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:runx1 /  del25  hg97|age:2.5 month|tissue:kidney", "GSM4792205", "GSM4792205: runx1 /  kidney1; Danio rerio; RNA Seq", "GSM4792205", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792205", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_null_4.1.cln.fq.gz runx1_del25_null_4.2.cln.fq.gz", "fastq fastq", 6973886556.0, 27674153.0, "GSM4792205 r1", "0:126 1:126", "A:1932833306;C:1502732434;G:1534451974;T:2003868842;N:0", 126, 126, null, null, 1932833306, 1502732434, 1534451974, 2003868842, 0, "SRX9139720", "SRS7381386", "SRA1126725", "GEO", "NHGRI", 2, 0.93692, 0.93786, 0.11567, 0.11588, 0.74123, 0.74099, 0.56167, 0.56297, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60919, "SRR12658661", "SRX9139719", "SRS7381385", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney3", "GSM4792204", null, "source name:adult kidney|strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "WT kidney3", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "GSM4792204", "GSM4792204: WT kidney3; Danio rerio; RNA Seq", "GSM4792204", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792204", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_WT_3.1.cln.fq.gz runx1_del25_WT_3.2.cln.fq.gz", "fastq fastq", 11183311944.0, 44378222.0, "GSM4792204 r1", "0:126 1:126", "A:2920698001;C:2577574528;G:2637485861;T:3047553554;N:0", 126, 126, null, null, 2920698001, 2577574528, 2637485861, 3047553554, 0, "SRX9139719", "SRS7381385", "SRA1126725", "GEO", "NHGRI", 2, 0.95338, 0.95426, 0.07656, 0.07667, 0.72693, 0.72782, 0.51199, 0.51082, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60920, "SRR12658660", "SRX9139718", "SRS7381384", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney2", "GSM4792203", null, "source name:adult kidney|strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "WT kidney2", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "GSM4792203", "GSM4792203: WT kidney2; Danio rerio; RNA Seq", "GSM4792203", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792203", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_WT_2.1.cln.fq.gz runx1_del25_WT_2.2.cln.fq.gz", "fastq fastq", 9052361388.0, 35922069.0, "GSM4792203 r1", "0:126 1:126", "A:2412816184;C:2041456610;G:2086024563;T:2512064031;N:0", 126, 126, null, null, 2412816184, 2041456610, 2086024563, 2512064031, 0, "SRX9139718", "SRS7381384", "SRA1126725", "GEO", "NHGRI", 2, 0.94726, 0.94854, 0.09295, 0.09312, 0.73198, 0.73206, 0.54429, 0.54313, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [60921, "SRR12658659", "SRX9139717", "SRS7381383", "SRP282671", "PRJNA663959", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development", "GSE158098", "Transcriptome Analysis", "Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 /  siblings 2.5 mpf  pool of 3 kidneys/replicate  n= 3 for each genotype.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney1", "GSM4792202", null, "source name:adult kidney|strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "WT kidney1", "RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.", "adult kidney", null, "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", null, "strain:EK|genotype/variation:WT|age:2.5 month|tissue:kidney", "GSM4792202", "GSM4792202: WT kidney1; Danio rerio; RNA Seq", "GSM4792202", null, "1", "RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in  80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.", "GEO Accession:GSM4792202", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282671", null, null, "runx1_del25_WT_1.1.cln.fq.gz runx1_del25_WT_1.2.cln.fq.gz", "fastq fastq", 10029561192.0, 39799846.0, "GSM4792202 r1", "0:126 1:126", "A:2618335131;C:2316817389;G:2358350895;T:2736057777;N:0", 126, 126, null, null, 2618335131, 2316817389, 2358350895, 2736057777, 0, "SRX9139717", "SRS7381383", "SRA1126725", "GEO", "NHGRI", 2, 0.95028, 0.95138, 0.08999, 0.09004, 0.77956, 0.78102, 0.54427, 0.5347, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-09-16", "Juvenile", "Juvenile", "Kidney", "Renal System"], [63833, "SRR14077612", "SRX10451897", "SRS8583182", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney3 [runx1]", "GSM5212431", null, "source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "WT kidney3 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212431", "GSM5212431: WT kidney3 [runx1]; Danio rerio; RNA Seq", "GSM5212431", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212431", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.5.8142700.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142700.2.cln.fq.gz", "fastq fastq", 5620598490.0, 22731446.0, "GSM5212431 r1", "0:123.63 1:123.63", "A:1519385372;C:1283859179;G:1297145256;T:1520155478;N:53205", 123, 123, null, null, 1519385372, 1283859179, 1297145256, 1520155478, 53205, "SRX10451897", "SRS8583182", "SRA1210911", "GEO", "NHGRI", 2, 0.94209, 0.94365, 0.1093, 0.10867, 0.7655, 0.76471, 0.52137, 0.52991, 57, 57, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [63834, "SRR14077613", "SRX10451897", "SRS8583182", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney3 [runx1]", "GSM5212431", null, "source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "WT kidney3 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212431", "GSM5212431: WT kidney3 [runx1]; Danio rerio; RNA Seq", "GSM5212431", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212431", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.4.8142700.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142700.2.cln.fq.gz", "fastq fastq", 5653835646.0, 22866105.0, "GSM5212431 r2", "0:123.63 1:123.63", "A:1528563748;C:1291263140;G:1304651524;T:1529275913;N:81321", 123, 123, null, null, 1528563748, 1291263140, 1304651524, 1529275913, 81321, "SRX10451897", "SRS8583182", "SRA1210911", "GEO", "NHGRI", 2, 0.94227, 0.9433, 0.10809, 0.1082, 0.7654, 0.76629, 0.46698, 0.51583, 120, 120, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [63835, "SRR14077610", "SRX10451896", "SRS8583181", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney2 [runx1]", "GSM5212430", null, "source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "WT kidney2 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212430", "GSM5212430: WT kidney2 [runx1]; Danio rerio; RNA Seq", "GSM5212430", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212430", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.4.8142702.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142702.2.cln.fq.gz", "fastq fastq", 5711423980.0, 23122476.0, "GSM5212430 r1", "0:123.50 1:123.50", "A:1541001316;C:1305691699;G:1320208515;T:1544438912;N:83538", 123, 123, null, null, 1541001316, 1305691699, 1320208515, 1544438912, 83538, "SRX10451896", "SRS8583181", "SRA1210911", "GEO", "NHGRI", 2, 0.95092, 0.95171, 0.07601, 0.07547, 0.73584, 0.73665, 0.45011, 0.45353, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [63836, "SRR14077611", "SRX10451896", "SRS8583181", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney2 [runx1]", "GSM5212430", null, "source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "WT kidney2 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212430", "GSM5212430: WT kidney2 [runx1]; Danio rerio; RNA Seq", "GSM5212430", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212430", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.5.8142702.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142702.2.cln.fq.gz", "fastq fastq", 5674131430.0, 22971228.0, "GSM5212430 r2", "0:123.51 1:123.51", "A:1530898067;C:1297222710;G:1311658561;T:1534297201;N:54891", 123, 123, null, null, 1530898067, 1297222710, 1311658561, 1534297201, 54891, "SRX10451896", "SRS8583181", "SRA1210911", "GEO", "NHGRI", 2, 0.95066, 0.95158, 0.07593, 0.07608, 0.73263, 0.7343, 0.44607, 0.44584, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [63837, "SRR14077608", "SRX10451895", "SRS8583180", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney1 [runx1]", "GSM5212429", null, "source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "WT kidney1 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212429", "GSM5212429: WT kidney1 [runx1]; Danio rerio; RNA Seq", "GSM5212429", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212429", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.5.8142698.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142698.2.cln.fq.gz", "fastq fastq", 6048097920.0, 24370362.0, "GSM5212429 r1", "0:124.09 1:124.09", "A:1630531156;C:1385676653;G:1399270262;T:1632562524;N:57325", 124, 124, null, null, 1630531156, 1385676653, 1399270262, 1632562524, 57325, "SRX10451895", "SRS8583180", "SRA1210911", "GEO", "NHGRI", 2, 0.94669, 0.94821, 0.09654, 0.09706, 0.73537, 0.73606, 0.49615, 0.49775, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [63838, "SRR14077609", "SRX10451895", "SRS8583180", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "WT kidney1 [runx1]", "GSM5212429", null, "source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "WT kidney1 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212429", "GSM5212429: WT kidney1 [runx1]; Danio rerio; RNA Seq", "GSM5212429", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212429", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.4.8142698.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142698.2.cln.fq.gz", "fastq fastq", 6086298924.0, 24523879.0, "GSM5212429 r2", "0:124.09 1:124.09", "A:1640963544;C:1394293929;G:1408031161;T:1642922398;N:87892", 124, 124, null, null, 1640963544, 1394293929, 1408031161, 1642922398, 87892, "SRX10451895", "SRS8583180", "SRA1210911", "GEO", "NHGRI", 2, 0.94597, 0.94665, 0.09708, 0.09725, 0.73744, 0.73839, 0.49464, 0.49315, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [63839, "SRR14077616", "SRX10451894", "SRS8583179", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney6 [runx1]", "GSM5212433", null, "source name:adult kidney|genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month", "runx1 /  kidney6 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212433", "GSM5212433: runx1 /  kidney6 [runx1]; Danio rerio; RNA Seq", "GSM5212433", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212433", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.4.8142704.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142704.2.cln.fq.gz", "fastq fastq", 5830417310.0, 23547116.0, "GSM5212433 r1", "0:123.80 1:123.80", "A:1528065414;C:1374560308;G:1389503409;T:1538204560;N:83619", 123, 123, null, null, 1528065414, 1374560308, 1389503409, 1538204560, 83619, "SRX10451894", "SRS8583179", "SRA1210911", "GEO", "NHGRI", 2, 0.94227, 0.9443, 0.0312, 0.03106, 0.7305, 0.73198, 0.4564, 0.45229, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [63840, "SRR14077617", "SRX10451894", "SRS8583179", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney6 [runx1]", "GSM5212433", null, "source name:adult kidney|genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month", "runx1 /  kidney6 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212433", "GSM5212433: runx1 /  kidney6 [runx1]; Danio rerio; RNA Seq", "GSM5212433", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212433", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.5.8142704.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142704.2.cln.fq.gz", "fastq fastq", 5801368354.0, 23428774.0, "GSM5212433 r2", "0:123.81 1:123.81", "A:1520440154;C:1367723047;G:1382629888;T:1530520601;N:54664", 123, 123, null, null, 1520440154, 1367723047, 1382629888, 1530520601, 54664, "SRX10451894", "SRS8583179", "SRA1210911", "GEO", "NHGRI", 2, 0.94318, 0.94442, 0.03018, 0.0303, 0.72835, 0.72906, 0.44351, 0.44657, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [63841, "SRR14077614", "SRX10451893", "SRS8583178", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney5 [runx1]", "GSM5212432", null, "source name:adult kidney|genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month", "runx1 /  kidney5 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212432", "GSM5212432: runx1 /  kidney5 [runx1]; Danio rerio; RNA Seq", "GSM5212432", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.5.8142695.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142695.2.cln.fq.gz", "fastq fastq", 5768438696.0, 23423221.0, "GSM5212432 r1", "0:123.14 1:123.14", "A:1566209291;C:1310337702;G:1323216779;T:1568619957;N:54967", 123, 123, null, null, 1566209291, 1310337702, 1323216779, 1568619957, 54967, "SRX10451893", "SRS8583178", "SRA1210911", "GEO", "NHGRI", 2, 0.94778, 0.94948, 0.0935, 0.09399, 0.72157, 0.72299, 0.49608, 0.49634, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [63842, "SRR14077615", "SRX10451893", "SRS8583178", "SRP312298", "PRJNA717672", "Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2]", "GSE169689", "Transcriptome Analysis", "Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.", "parent bioproject:PRJNA663961", "pubmed:34492681", null, "runx1 /  kidney5 [runx1]", "GSM5212432", null, "source name:adult kidney|genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month", "runx1 /  kidney5 [runx1]", "RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts", "adult kidney", null, "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", null, "genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month", "GSM5212432", "GSM5212432: runx1 /  kidney5 [runx1]; Danio rerio; RNA Seq", "GSM5212432", null, "1", "Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52\uf0b0C for 10 min and then overnight in  80\uf0b0C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2", "GEO Accession:GSM5212432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312298", null, null, "141031_OPTIMUS_C5M4FANXX.4.8142695.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142695.2.cln.fq.gz", "fastq fastq", 5808145902.0, 23584233.0, "GSM5212432 r2", "0:123.14 1:123.14", "A:1576938864;C:1319376550;G:1332344310;T:1579402358;N:83820", 123, 123, null, null, 1576938864, 1319376550, 1332344310, 1579402358, 83820, "SRX10451893", "SRS8583178", "SRA1210911", "GEO", "NHGRI", 2, 0.94737, 0.94902, 0.09296, 0.09311, 0.72228, 0.7236, 0.49544, 0.48947, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-26", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [76969, "SRR25411155", "SRX21146780", "SRS18409873", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep2", "GSM7659931", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659931", "GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq", "GSM7659931 r1", "GSM7659931", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep2_CCGTCC_L001_R1_001.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659931 r1", "0:51", "A:53477924;C:49271060;G:48329809;T:52644666;N:276541", 51, null, null, null, 53477924, 49271060, 48329809, 52644666, 276541, "SRX21146780", "SRS18409873", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90949, null, 0.04979, null, 0.78616, null, 0.46807, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76970, "SRR25411156", "SRX21146780", "SRS18409873", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep2", "GSM7659931", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659931", "GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq", "GSM7659931 r1", "GSM7659931", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep2_CCGTCC_L001_R1_002.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659931 r2", "0:51", "A:53509907;C:49243113;G:48349675;T:52646358;N:250947", 51, null, null, null, 53509907, 49243113, 48349675, 52646358, 250947, "SRX21146780", "SRS18409873", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90721, null, 0.04855, null, 0.78614, null, 0.49297, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76971, "SRR25411157", "SRX21146780", "SRS18409873", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep2", "GSM7659931", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659931", "GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq", "GSM7659931 r1", "GSM7659931", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep2_CCGTCC_L001_R1_003.fastq.gz", "fastq", 184894839.0, 3625389.0, "GSM7659931 r3", "0:51", "A:48502504;C:44662414;G:43793127;T:47769015;N:167779", 51, null, null, null, 48502504, 44662414, 43793127, 47769015, 167779, "SRX21146780", "SRS18409873", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90939, null, 0.04945, null, 0.78413, null, 0.50176, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76972, "SRR25411158", "SRX21146780", "SRS18409873", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep2", "GSM7659931", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659931", "GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq", "GSM7659931 r1", "GSM7659931", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep2_CCGTCC_L002_R1_001.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659931 r4", "0:51", "A:53524100;C:49307589;G:48369558;T:52683611;N:115142", 51, null, null, null, 53524100, 49307589, 48369558, 52683611, 115142, "SRX21146780", "SRS18409873", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90886, null, 0.04911, null, 0.78563, null, 0.50213, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76973, "SRR25411159", "SRX21146780", "SRS18409873", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep2", "GSM7659931", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659931", "GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq", "GSM7659931 r1", "GSM7659931", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep2_CCGTCC_L002_R1_002.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659931 r5", "0:51", "A:53508602;C:49259259;G:48320396;T:52659338;N:252405", 51, null, null, null, 53508602, 49259259, 48320396, 52659338, 252405, "SRX21146780", "SRS18409873", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90952, null, 0.04948, null, 0.78476, null, 0.50006, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76974, "SRR25411160", "SRX21146780", "SRS18409873", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep2", "GSM7659931", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659931", "GSM7659931: RNAseq 4month tet2 wt rep2; Danio rerio; RNA Seq", "GSM7659931 r1", "GSM7659931", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep2_CCGTCC_L002_R1_003.fastq.gz", "fastq", 193938618.0, 3802718.0, "GSM7659931 r6", "0:51", "A:50925302;C:46847931;G:45921088;T:50125614;N:118683", 51, null, null, null, 50925302, 46847931, 45921088, 50125614, 118683, "SRX21146780", "SRS18409873", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90989, null, 0.04933, null, 0.78612, null, 0.49518, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76975, "SRR25411161", "SRX21146779", "SRS18409872", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep1", "GSM7659928", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659928", "GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq", "GSM7659928 r1", "GSM7659928", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep1_AGTCAA_L001_R1_001.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659928 r1", "0:51", "A:55015856;C:47764328;G:46586189;T:54347107;N:286520", 51, null, null, null, 55015856, 47764328, 46586189, 54347107, 286520, "SRX21146779", "SRS18409872", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.94153, null, 0.06397, null, 0.7679, null, 0.51518, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76976, "SRR25411162", "SRX21146779", "SRS18409872", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep1", "GSM7659928", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659928", "GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq", "GSM7659928 r1", "GSM7659928", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep1_AGTCAA_L001_R1_002.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659928 r2", "0:51", "A:55049694;C:47738867;G:46600712;T:54359486;N:251241", 51, null, null, null, 55049694, 47738867, 46600712, 54359486, 251241, "SRX21146779", "SRS18409872", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.93994, null, 0.06362, null, 0.76771, null, 0.51436, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76977, "SRR25411163", "SRX21146779", "SRS18409872", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep1", "GSM7659928", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659928", "GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq", "GSM7659928 r1", "GSM7659928", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep1_AGTCAA_L001_R1_003.fastq.gz", "fastq", 184542582.0, 3618482.0, "GSM7659928 r3", "0:51", "A:49810884;C:43215836;G:42140250;T:49210846;N:164766", 51, null, null, null, 49810884, 43215836, 42140250, 49210846, 164766, "SRX21146779", "SRS18409872", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.94126, null, 0.06349, null, 0.76609, null, 0.50688, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76978, "SRR25411164", "SRX21146779", "SRS18409872", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep1", "GSM7659928", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659928", "GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq", "GSM7659928 r1", "GSM7659928", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep1_AGTCAA_L002_R1_001.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659928 r4", "0:51", "A:55088455;C:47783649;G:46637795;T:54374341;N:115760", 51, null, null, null, 55088455, 47783649, 46637795, 54374341, 115760, "SRX21146779", "SRS18409872", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.94226, null, 0.06408, null, 0.76727, null, 0.48927, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76979, "SRR25411165", "SRX21146779", "SRS18409872", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep1", "GSM7659928", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659928", "GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq", "GSM7659928 r1", "GSM7659928", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep1_AGTCAA_L002_R1_002.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659928 r5", "0:51", "A:55050408;C:47744731;G:46583753;T:54358628;N:262480", 51, null, null, null, 55050408, 47744731, 46583753, 54358628, 262480, "SRX21146779", "SRS18409872", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.94149, null, 0.06416, null, 0.7671, null, 0.50616, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76980, "SRR25411166", "SRX21146779", "SRS18409872", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep1", "GSM7659928", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659928", "GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq", "GSM7659928 r1", "GSM7659928", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep1_AGTCAA_L002_R1_003.fastq.gz", "fastq", 192468441.0, 3773891.0, "GSM7659928 r6", "0:51", "A:51989979;C:45058442;G:43960412;T:51339541;N:120067", 51, null, null, null, 51989979, 45058442, 43960412, 51339541, 120067, "SRX21146779", "SRS18409872", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.94177, null, 0.06438, null, 0.76751, null, 0.50837, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76981, "SRR25411167", "SRX21146778", "SRS18409871", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep1", "GSM7659930", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659930", "GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq", "GSM7659930 r1", "GSM7659930", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep1_TGACCA_L001_R1_001.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659930 r1", "0:51", "A:54329942;C:48443007;G:47297646;T:53631114;N:298291", 51, null, null, null, 54329942, 48443007, 47297646, 53631114, 298291, "SRX21146778", "SRS18409871", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90366, null, 0.06258, null, 0.76958, null, 0.48257, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76982, "SRR25411168", "SRX21146778", "SRS18409871", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep1", "GSM7659930", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659930", "GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq", "GSM7659930 r1", "GSM7659930", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep1_TGACCA_L001_R1_002.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659930 r2", "0:51", "A:54383177;C:48419596;G:47328645;T:53626949;N:241633", 51, null, null, null, 54383177, 48419596, 47328645, 53626949, 241633, "SRX21146778", "SRS18409871", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90117, null, 0.06248, null, 0.77064, null, 0.51114, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76983, "SRR25411169", "SRX21146778", "SRS18409871", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep1", "GSM7659930", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659930", "GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq", "GSM7659930 r1", "GSM7659930", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep1_TGACCA_L001_R1_003.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659930 r3", "0:51", "A:54382835;C:48432142;G:47310240;T:53688971;N:185812", 51, null, null, null, 54382835, 48432142, 47310240, 53688971, 185812, "SRX21146778", "SRS18409871", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90404, null, 0.06341, null, 0.76962, null, 0.48176, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76984, "SRR25411170", "SRX21146778", "SRS18409871", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep1", "GSM7659930", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659930", "GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq", "GSM7659930 r1", "GSM7659930", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep1_TGACCA_L001_R1_004.fastq.gz", "fastq", 22952397.0, 450047.0, "GSM7659930 r4", "0:51", "A:6123383;C:5438458;G:5312317;T:6056716;N:21523", 51, null, null, null, 6123383, 5438458, 5312317, 6056716, 21523, "SRX21146778", "SRS18409871", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90219, null, 0.06393, null, 0.77068, null, 0.50827, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76985, "SRR25411171", "SRX21146778", "SRS18409871", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep1", "GSM7659930", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659930", "GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq", "GSM7659930 r1", "GSM7659930", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep1_TGACCA_L002_R1_001.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659930 r5", "0:51", "A:54377430;C:48474926;G:47349887;T:53685203;N:112554", 51, null, null, null, 54377430, 48474926, 47349887, 53685203, 112554, "SRX21146778", "SRS18409871", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90473, null, 0.06338, null, 0.77023, null, 0.50688, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76986, "SRR25411172", "SRX21146778", "SRS18409871", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep1", "GSM7659930", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659930", "GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq", "GSM7659930 r1", "GSM7659930", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep1_TGACCA_L002_R1_002.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659930 r6", "0:51", "A:54337748;C:48437652;G:47307297;T:53646000;N:271303", 51, null, null, null, 54337748, 48437652, 47307297, 53646000, 271303, "SRX21146778", "SRS18409871", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.9051, null, 0.06323, null, 0.76966, null, 0.50455, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76987, "SRR25411173", "SRX21146778", "SRS18409871", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep1", "GSM7659930", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659930", "GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq", "GSM7659930 r1", "GSM7659930", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep1_TGACCA_L002_R1_003.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659930 r7", "0:51", "A:54394822;C:48436830;G:47326355;T:53713847;N:128146", 51, null, null, null, 54394822, 48436830, 47326355, 53713847, 128146, "SRX21146778", "SRS18409871", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90342, null, 0.06243, null, 0.76917, null, 0.51036, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76988, "SRR25411174", "SRX21146778", "SRS18409871", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 wt rep1", "GSM7659930", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:WT|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 wt rep1", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:WT", "GSM7659930", "GSM7659930: RNAseq 4month tet2 wt rep1; Danio rerio; RNA Seq", "GSM7659930 r1", "GSM7659930", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_wt_rep1_TGACCA_L002_R1_004.fastq.gz", "fastq", 31292886.0, 613586.0, "GSM7659930 r8", "0:51", "A:8353864;C:7422258;G:7241468;T:8258321;N:16975", 51, null, null, null, 8353864, 7422258, 7241468, 8258321, 16975, "SRX21146778", "SRS18409871", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.90474, null, 0.06355, null, 0.77049, null, 0.5033, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76989, "SRR25411175", "SRX21146777", "SRS18409870", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep2", "GSM7659929", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659929", "GSM7659929: RNAseq 4month tet2 mut rep2; Danio rerio; RNA Seq", "GSM7659929 r1", "GSM7659929", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep2_GTGAAA_L001_R1_001.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659929 r1", "0:51", "A:55281308;C:47482302;G:46328343;T:54603495;N:304552", 51, null, null, null, 55281308, 47482302, 46328343, 54603495, 304552, "SRX21146777", "SRS18409870", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.93384, null, 0.06735, null, 0.7698, null, 0.50166, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76990, "SRR25411176", "SRX21146777", "SRS18409870", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep2", "GSM7659929", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659929", "GSM7659929: RNAseq 4month tet2 mut rep2; Danio rerio; RNA Seq", "GSM7659929 r1", "GSM7659929", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep2_GTGAAA_L001_R1_002.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659929 r2", "0:51", "A:55296032;C:47496692;G:46371124;T:54607512;N:228640", 51, null, null, null, 55296032, 47496692, 46371124, 54607512, 228640, "SRX21146777", "SRS18409870", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.92981, null, 0.06756, null, 0.77137, null, 0.49105, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76991, "SRR25411177", "SRX21146777", "SRS18409870", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep2", "GSM7659929", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659929", "GSM7659929: RNAseq 4month tet2 mut rep2; Danio rerio; RNA Seq", "GSM7659929 r1", "GSM7659929", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep2_GTGAAA_L001_R1_003.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659929 r3", "0:51", "A:55348684;C:47478537;G:46321354;T:54664188;N:187237", 51, null, null, null, 55348684, 47478537, 46321354, 54664188, 187237, "SRX21146777", "SRS18409870", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.93311, null, 0.06863, null, 0.77064, null, 0.49092, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76992, "SRR25411178", "SRX21146777", "SRS18409870", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep2", "GSM7659929", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659929", "GSM7659929: RNAseq 4month tet2 mut rep2; Danio rerio; RNA Seq", "GSM7659929 r1", "GSM7659929", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep2_GTGAAA_L001_R1_004.fastq.gz", "fastq", 73939443.0, 1449793.0, "GSM7659929 r4", "0:51", "A:20056823;C:17197480;G:16767822;T:19830159;N:87159", 51, null, null, null, 20056823, 17197480, 16767822, 19830159, 87159, "SRX21146777", "SRS18409870", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.93293, null, 0.06846, null, 0.77074, null, 0.49688, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76993, "SRR25411179", "SRX21146777", "SRS18409870", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep2", "GSM7659929", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659929", "GSM7659929: RNAseq 4month tet2 mut rep2; Danio rerio; RNA Seq", "GSM7659929 r1", "GSM7659929", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep2_GTGAAA_L002_R1_001.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659929 r5", "0:51", "A:55324316;C:47529509;G:46377670;T:54659998;N:108507", 51, null, null, null, 55324316, 47529509, 46377670, 54659998, 108507, "SRX21146777", "SRS18409870", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.93294, null, 0.06692, null, 0.76926, null, 0.49901, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76994, "SRR25411180", "SRX21146777", "SRS18409870", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep2", "GSM7659929", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659929", "GSM7659929: RNAseq 4month tet2 mut rep2; Danio rerio; RNA Seq", "GSM7659929 r1", "GSM7659929", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP451262", null, null, "RNAseq_4month_tet2_mut_rep2_GTGAAA_L002_R1_002.fastq.gz", "fastq", 204000000.0, 4000000.0, "GSM7659929 r6", "0:51", "A:55318795;C:47459834;G:46311380;T:54653184;N:256807", 51, null, null, null, 55318795, 47459834, 46311380, 54653184, 256807, "SRX21146777", "SRS18409870", "SRA1679257", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", "Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia", 1, 0.93279, null, 0.0681, null, 0.77108, null, 0.49482, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2023-07-25", "Adult", "Adult", "Kidney", "Renal System"], [76995, "SRR25411181", "SRX21146777", "SRS18409870", "SRP451262", "PRJNA998264", "Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq]", "GSE238175", "Transcriptome Analysis", "Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis  cytopenias and dysplasia. The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep2", "GSM7659929", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. 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The gene encoding Ten ele\u00acven translocation 2 TET2  a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine  is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously  we reported a stable zebrafish line with a loss of function mutation in the tet2 gene.  The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study  we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further  hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2   involved in polycomb repressive complex 2 PRC2. However  between 4 month and 15 month of age  however  we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation  heme metabolism  and IL2/STAT5 signaling  possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally  there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome", "parent bioproject:PRJNA998260", "pubmed:37937078", null, "RNAseq 4month tet2 mut rep2", "GSM7659929", null, "source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing", "RNAseq 4month tet2 mut rep2", "Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing  the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene", "Kidney", null, "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant", "GSM7659929", "GSM7659929: RNAseq 4month tet2 mut rep2; Danio rerio; RNA Seq", "GSM7659929 r1", "GSM7659929", "1", "RNA was extracted  from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", 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