{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" and tissue_curation = \"Kidney\"", "rows": [[10166, "ERR5762357", "ERX5471113", "ERS6291553", "ERP128548", "PRJEB44492", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E-MTAB-10370", "Transcriptome Analysis", "GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.", "wt2 gata2b", "SAMEA8606934", "Erasmus Medical Center", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606934|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt2 gata2b|sampling site:kidney marrow|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E MTAB 10370:wt2 gata2b p", "wt2 gata2b p", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128548", "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", "wt2_gata2b.bam", "bam", 25266437196.0, 277653156.0, "E MTAB 10370:wt2 gata2b", "0:91", "A:7555470312;C:5144518052;G:5682746714;T:6882396490;N:1305628", 91, null, null, null, 7555470312, 5144518052, 5682746714, 6882396490, 1305628, "ERX5471113", "ERS6291553", "ERA4089475", "Erasmus Medical Center|European Nucleotide Archive", "Erasmus Medical Center|European Nucleotide Archive", 1, 0.90876, null, 0.18424, null, 0.84017, null, 0.55508, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Netherlands", "2022-04-09", "Adult", "Adult", "Kidney", "Renal System"], [10167, "ERR5762356", "ERX5471112", "ERS6291552", "ERP128548", "PRJEB44492", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E-MTAB-10370", "Transcriptome Analysis", "GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.", "wt1 gata2b", "SAMEA8606933", "Erasmus Medical Center", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606933|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt1 gata2b|sampling site:kidney marrow|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E MTAB 10370:wt1 gata2b p", "wt1 gata2b p", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128548", "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", "wt1_gata2b.bam", "bam", 36376708095.0, 399744045.0, "E MTAB 10370:wt1 gata2b", "0:91", "A:10397161431;C:8128518427;G:8799445454;T:9049686061;N:1896722", 91, null, null, null, 10397161431, 8128518427, 8799445454, 9049686061, 1896722, "ERX5471112", "ERS6291552", "ERA4089475", "Erasmus Medical Center|European Nucleotide Archive", "Erasmus Medical Center|European Nucleotide Archive", 1, 0.94708, null, 0.08938, null, 0.85449, null, 0.52917, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Netherlands", "2022-04-09", "Adult", "Adult", "Kidney", "Renal System"], [10168, "ERR5762355", "ERX5471111", "ERS6291551", "ERP128548", "PRJEB44492", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E-MTAB-10370", "Transcriptome Analysis", "GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.", "hom2 gata2b", "SAMEA8606932", "Erasmus Medical Center", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606932|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom2 gata2b|sampling site:kidney marrow|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E MTAB 10370:hom2 gata2b p", "hom2 gata2b p", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.", "Experimental Factor: genotype:gata2b / ", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128548", "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", "hom2_gata2b.bam", "bam", 22416887402.0, 246339422.0, "E MTAB 10370:hom2 gata2b", "0:91", "A:6732382430;C:4540586585;G:4933684272;T:6209137814;N:1096301", 91, null, null, null, 6732382430, 4540586585, 4933684272, 6209137814, 1096301, "ERX5471111", "ERS6291551", "ERA4089475", "Erasmus Medical Center|European Nucleotide Archive", "Erasmus Medical Center|European Nucleotide Archive", 1, 0.91306, null, 0.21566, null, 0.83469, null, 0.53782, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Netherlands", "2022-04-09", "Adult", "Adult", "Kidney", "Renal System"], [10169, "ERR5762354", "ERX5471110", "ERS6291550", "ERP128548", "PRJEB44492", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E-MTAB-10370", "Transcriptome Analysis", "GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.", "hom1 gata2b", "SAMEA8606931", "Erasmus Medical Center", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606931|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom1 gata2b|sampling site:kidney marrow|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E MTAB 10370:hom1 gata2b p", "hom1 gata2b p", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.", "Experimental Factor: genotype:gata2b / ", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128548", "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", "hom1_gata2b.bam", "bam", 18004290759.0, 197849349.0, "E MTAB 10370:hom1 gata2b", "0:91", "A:5232521408;C:3876317502;G:4287902596;T:4606191653;N:1357600", 91, null, null, null, 5232521408, 3876317502, 4287902596, 4606191653, 1357600, "ERX5471110", "ERS6291550", "ERA4089475", "Erasmus Medical Center|European Nucleotide Archive", "Erasmus Medical Center|European Nucleotide Archive", 1, 0.94131, null, 0.08871, null, 0.83465, null, 0.52792, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Netherlands", "2022-04-09", "Adult", "Adult", "Kidney", "Renal System"], [25326, "SRR25868015", "SRX21589423", "SRS18766996", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "vaccinated+SVCV  scRNAseq Kidney leukocyte", "GSM7749529", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV|geo loc name:missing|collection date:missing", "vaccinated+SVCV  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV", "GSM7749529", "GSM7749529: vaccinated+SVCV  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749529 r1", "GSM7749529", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "vaccinated+SVCV_S1_L001_R1_001.fastq.gz vaccinated+SVCV_S1_L001_R2_001.fastq.gz", "fastq fastq", 48964415682.0, 411465678.0, "GSM7749529 r1", "0:28 1:91", "A:13575624351;C:10984755198;G:11582424564;T:12820058148;N:1553421", 28, 91, null, null, 13575624351, 10984755198, 11582424564, 12820058148, 1553421, "SRX21589423", "SRS18766996", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00754, 0.93029, 0.00274, 0.13414, 0.99168, 0.81527, 0.35, 0.50044, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [25327, "SRR25868016", "SRX21589422", "SRS18766995", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "SVCV  scRNAseq Kidney leukocyte", "GSM7749528", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV|geo loc name:missing|collection date:missing", "SVCV  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV", "GSM7749528", "GSM7749528: SVCV  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749528 r1", "GSM7749528", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "SVCV_S1_L001_R2_001.fastq.gz SVCV_S1_L001_R1_001.fastq.gz", "fastq fastq", 48037908933.0, 403679907.0, "GSM7749528 r1", "0:28 1:91", "A:13476452185;C:10712519121;G:11200837365;T:12646404590;N:1695672", 28, 91, null, null, 13476452185, 10712519121, 11200837365, 12646404590, 1695672, "SRX21589422", "SRS18766995", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00795, 0.92383, 0.00261, 0.14, 0.98948, 0.7806, 0.36862, 0.54549, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [25328, "SRR25868017", "SRX21589421", "SRS18766994", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "PBS  scRNAseq Kidney leukocyte", "GSM7749527", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS|geo loc name:missing|collection date:missing", "PBS  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS", "GSM7749527", "GSM7749527: PBS  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749527 r1", "GSM7749527", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "PBS_S1_L001_R1_001.fastq.gz PBS_S1_L001_R2_001.fastq.gz", "fastq fastq", 49559940115.0, 416470085.0, "GSM7749527 r1", "0:28 1:91", "A:13856071803;C:11114011608;G:11616674427;T:12971434952;N:1747325", 28, 91, null, null, 13856071803, 11114011608, 11616674427, 12971434952, 1747325, "SRX21589421", "SRS18766994", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00648, 0.92681, 0.00213, 0.1376, 0.99056, 0.79866, 0.40117, 0.5487, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [28589, "SRR26491369", "SRX22195232", "SRS19251247", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "KM eos", "GSM7854254", null, "source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "KM eos", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "eosinophils", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854254", "GSM7854254: KM eos; Danio rerio; RNA Seq", "GSM7854254 r1", "GSM7854254", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "LGF-2-LGF-2-1_L1_1.fq.gz LGF-2-LGF-2-1_L1_2.fq.gz", "fastq fastq", 25680257100.0, 85600857.0, "GSM7854254 r1", "0:150 1:150", "A:8025239149;C:3737115767;G:4237725481;T:9679701617;N:475086", 150, 150, null, null, 8025239149, 3737115767, 4237725481, 9679701617, 475086, "SRX22195232", "SRS19251247", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.21477, 0.87303, 0.06136, 0.18991, 0.99084, 0.83187, 0.58742, 0.60309, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28590, "SRR26491370", "SRX22195232", "SRS19251247", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "KM eos", "GSM7854254", null, "source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "KM eos", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "eosinophils", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854254", "GSM7854254: KM eos; Danio rerio; RNA Seq", "GSM7854254 r1", "GSM7854254", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "LGF-2-LGF-2-2_L1_1.fq.gz LGF-2-LGF-2-2_L1_2.fq.gz", "fastq fastq", 30035236200.0, 100117454.0, "GSM7854254 r2", "0:150 1:150", "A:9382913917;C:4364910890;G:4955266285;T:11331735278;N:409830", 150, 150, null, null, 9382913917, 4364910890, 4955266285, 11331735278, 409830, "SRX22195232", "SRS19251247", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.20279, 0.87187, 0.05971, 0.19015, 0.99068, 0.83108, 0.6129, 0.60029, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28591, "SRR26491371", "SRX22195232", "SRS19251247", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "KM eos", "GSM7854254", null, "source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "KM eos", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "eosinophils", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854254", "GSM7854254: KM eos; Danio rerio; RNA Seq", "GSM7854254 r1", "GSM7854254", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "LGF-2-LGF-2-3_L1_1.fq.gz LGF-2-LGF-2-3_L1_2.fq.gz", "fastq fastq", 29383046400.0, 97943488.0, "GSM7854254 r3", "0:150 1:150", "A:9183968085;C:4275116661;G:4844377300;T:11079048598;N:535756", 150, 150, null, null, 9183968085, 4275116661, 4844377300, 11079048598, 535756, "SRX22195232", "SRS19251247", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.19524, 0.87384, 0.06096, 0.19095, 0.99188, 0.83293, 0.58701, 0.58361, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28592, "SRR26491372", "SRX22195232", "SRS19251247", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "KM eos", "GSM7854254", null, "source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "KM eos", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "eosinophils", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854254", "GSM7854254: KM eos; Danio rerio; RNA Seq", "GSM7854254 r1", "GSM7854254", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "LGF-2-LGF-2-4_L1_1.fq.gz LGF-2-LGF-2-4_L1_2.fq.gz", "fastq fastq", 33167265900.0, 110557553.0, "GSM7854254 r4", "0:150 1:150", "A:10380451186;C:4827987987;G:5467300098;T:12490912690;N:613939", 150, 150, null, null, 10380451186, 4827987987, 5467300098, 12490912690, 613939, "SRX22195232", "SRS19251247", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.21222, 0.87102, 0.06704, 0.18877, 0.99052, 0.83343, 0.56053, 0.58249, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28593, "SRR26491373", "SRX22195231", "SRS19251246", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 3", "GSM7854253", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 3", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854253", "GSM7854253: cebpb mut KM 3; Danio rerio; RNA Seq", "GSM7854253 r1", "GSM7854253", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "b3_S0_L003_R2_001.fastq.gz b3_S0_L003_R1_001.fastq.gz", "fastq fastq", 112688609700.0, 375628699.0, "GSM7854253 r1", "0:150 1:150", "A:38960384866;C:23864873253;G:24209853889;T:25652339570;N:1158122", 150, 150, null, null, 38960384866, 23864873253, 24209853889, 25652339570, 1158122, "SRX22195231", "SRS19251246", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.89036, 0.0, 0.11804, 1.0, 0.86318, null, 0.69315, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28594, "SRR26491374", "SRX22195230", "SRS19251245", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 2", "GSM7854252", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 2", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854252", "GSM7854252: cebpb mut KM 2; Danio rerio; RNA Seq", "GSM7854252 r1", "GSM7854252", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "b2_S0_L003_R1_001.fastq.gz b2_S0_L003_R2_001.fastq.gz", "fastq fastq", 115982411700.0, 386608039.0, "GSM7854252 r1", "0:150 1:150", "A:39966143944;C:23813985234;G:22925287805;T:29275806145;N:1188572", 150, 150, null, null, 39966143944, 23813985234, 22925287805, 29275806145, 1188572, "SRX22195230", "SRS19251245", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86607, 0.0, 0.12954, 1.0, 0.83132, null, 0.631, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28595, "SRR26491375", "SRX22195229", "SRS19251244", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 1", "GSM7854251", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854251", "GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq", "GSM7854251 r1", "GSM7854251", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KMB-KMB-1_FKDL210332848-1a-AK4437_1.fq.gz KMB-KMB-1_FKDL210332848-1a-AK4437_2.fq.gz", "fastq fastq", 17042007300.0, 56806691.0, "GSM7854251 r1", "0:150 1:150", "A:5668533017;C:3385304499;G:3366957982;T:4620992880;N:218922", 150, 150, null, null, 5668533017, 3385304499, 3366957982, 4620992880, 218922, "SRX22195229", "SRS19251244", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.03184, 0.89149, 0.00867, 0.11757, 0.99758, 0.82077, 0.751, 0.57147, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28596, "SRR26491376", "SRX22195229", "SRS19251244", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 1", "GSM7854251", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854251", "GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq", "GSM7854251 r1", "GSM7854251", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KMB-KMB-2_FKDL210332848-1a-AK4438_1.fq.gz KMB-KMB-2_FKDL210332848-1a-AK4438_2.fq.gz", "fastq fastq", 16343762400.0, 54479208.0, "GSM7854251 r2", "0:150 1:150", "A:5450512159;C:3242501005;G:3220219102;T:4430319009;N:211125", 150, 150, null, null, 5450512159, 3242501005, 3220219102, 4430319009, 211125, "SRX22195229", "SRS19251244", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.02568, 0.8936, 0.00694, 0.11929, 0.99776, 0.82235, 0.66666, 0.57382, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28597, "SRR26491377", "SRX22195229", "SRS19251244", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 1", "GSM7854251", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854251", "GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq", "GSM7854251 r1", "GSM7854251", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KMB-KMB-3_FKDL210332848-1a-AK4439_1.fq.gz KMB-KMB-3_FKDL210332848-1a-AK4439_2.fq.gz", "fastq fastq", 10959163500.0, 36530545.0, "GSM7854251 r3", "0:150 1:150", "A:3642539220;C:2179136896;G:2168295053;T:2969053386;N:138945", 150, 150, null, null, 3642539220, 2179136896, 2168295053, 2969053386, 138945, "SRX22195229", "SRS19251244", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.03232, 0.89137, 0.00922, 0.12039, 0.9974, 0.82171, 0.58775, 0.57177, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28598, "SRR26491378", "SRX22195229", "SRS19251244", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 1", "GSM7854251", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854251", "GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq", "GSM7854251 r1", "GSM7854251", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KMB-KMB-4_FKDL210332848-1a-AK4440_1.fq.gz KMB-KMB-4_FKDL210332848-1a-AK4440_2.fq.gz", "fastq fastq", 18130067100.0, 60433557.0, "GSM7854251 r4", "0:150 1:150", "A:6030347851;C:3607618024;G:3589047945;T:4902820241;N:233039", 150, 150, null, null, 6030347851, 3607618024, 3589047945, 4902820241, 233039, "SRX22195229", "SRS19251244", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.02563, 0.89333, 0.00745, 0.11784, 0.99805, 0.82156, 0.71568, 0.56377, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28599, "SRR26491379", "SRX22195228", "SRS19251243", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 3", "GSM7854250", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 3", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854250", "GSM7854250: cebp1 mut KM 3; Danio rerio; RNA Seq", "GSM7854250 r1", "GSM7854250", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "e3_S0_L003_R1_001.fastq.gz e3_S0_L003_R2_001.fastq.gz", "fastq fastq", 106692684600.0, 355642282.0, "GSM7854250 r1", "0:150 1:150", "A:43760768907;C:19045349028;G:18701042387;T:25183159362;N:2364916", 150, 150, null, null, 43760768907, 19045349028, 18701042387, 25183159362, 2364916, "SRX22195228", "SRS19251243", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.90163, 0.0, 0.08054, 1.0, 0.7908, null, 0.55652, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28600, "SRR26491380", "SRX22195227", "SRS19251242", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 2", "GSM7854249", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 2", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854249", "GSM7854249: cebp1 mut KM 2; Danio rerio; RNA Seq", "GSM7854249 r1", "GSM7854249", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "e2_S0_L003_R2_001.fastq.gz e2_S0_L003_R1_001.fastq.gz", "fastq fastq", 126515726100.0, 421719087.0, "GSM7854249 r1", "0:150 1:150", "A:44391473513;C:24602183317;G:23721160983;T:33799587611;N:1320676", 150, 150, null, null, 44391473513, 24602183317, 23721160983, 33799587611, 1320676, "SRX22195227", "SRS19251242", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.90423, 0.0, 0.07758, 1.0, 0.81509, null, 0.5598, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28601, "SRR26491381", "SRX22195226", "SRS19251241", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 1", "GSM7854248", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854248", "GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq", "GSM7854248 r1", "GSM7854248", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KM1-KM1-1_FKDL210332847-1a-AK4772_2.fq.gz KM1-KM1-1_FKDL210332847-1a-AK4772_1.fq.gz", "fastq fastq", 18653393400.0, 62177978.0, "GSM7854248 r1", "0:150 1:150", "A:6381285195;C:3802506730;G:3637919666;T:4831413881;N:267928", 150, 150, null, null, 6381285195, 3802506730, 3637919666, 4831413881, 267928, "SRX22195226", "SRS19251241", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86906, 0.0, 0.0958, 1.0, 0.84423, null, 0.5956, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28602, "SRR26491382", "SRX22195226", "SRS19251241", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 1", "GSM7854248", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854248", "GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq", "GSM7854248 r1", "GSM7854248", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KM1-KM1-2_FKDL210332847-1a-AK4773_1.fq.gz KM1-KM1-2_FKDL210332847-1a-AK4773_2.fq.gz", "fastq fastq", 18326971500.0, 61089905.0, "GSM7854248 r2", "0:150 1:150", "A:6267364051;C:3758542961;G:3587627310;T:4713172477;N:264701", 150, 150, null, null, 6267364051, 3758542961, 3587627310, 4713172477, 264701, "SRX22195226", "SRS19251241", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86638, 0.0, 0.09499, 1.0, 0.84526, null, 0.60651, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28603, "SRR26491383", "SRX22195226", "SRS19251241", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 1", "GSM7854248", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854248", "GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq", "GSM7854248 r1", "GSM7854248", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KM1-KM1-3_FKDL210332847-1a-AK4774_1.fq.gz KM1-KM1-3_FKDL210332847-1a-AK4774_2.fq.gz", "fastq fastq", 11808660600.0, 39362202.0, "GSM7854248 r3", "0:150 1:150", "A:4038900150;C:2417395586;G:2308989220;T:3043205908;N:169736", 150, 150, null, null, 4038900150, 2417395586, 2308989220, 3043205908, 169736, "SRX22195226", "SRS19251241", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86661, 0.0, 0.09574, 1.0, 0.84542, null, 0.57797, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28604, "SRR26491384", "SRX22195226", "SRS19251241", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 1", "GSM7854248", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854248", "GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq", "GSM7854248 r1", "GSM7854248", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KM1-KM1-4_FKDL210332847-1a-AK4775_1.fq.gz KM1-KM1-4_FKDL210332847-1a-AK4775_2.fq.gz", "fastq fastq", 13766583900.0, 45888613.0, "GSM7854248 r4", "0:150 1:150", "A:4706562659;C:2817183636;G:2693650162;T:3548993544;N:193899", 150, 150, null, null, 4706562659, 2817183636, 2693650162, 3548993544, 193899, "SRX22195226", "SRS19251241", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86464, 0.0, 0.09455, 1.0, 0.84453, null, 0.59712, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28605, "SRR26491385", "SRX22195225", "SRS19251240", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 3", "GSM7854247", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 3", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854247", "GSM7854247: WT KM 3; Danio rerio; RNA Seq", "GSM7854247 r1", "GSM7854247", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "w3_S0_L003_R1_001.fastq.gz w3_S0_L003_R2_001.fastq.gz", "fastq fastq", 142550442300.0, 475168141.0, "GSM7854247 r1", "0:150 1:150", "A:56961713939;C:27160797921;G:25876430130;T:32548386896;N:3113414", 150, 150, null, null, 56961713939, 27160797921, 25876430130, 32548386896, 3113414, "SRX22195225", "SRS19251240", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.84672, 0.0, 0.09057, 1.0, 0.84893, null, 0.64916, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28606, "SRR26491386", "SRX22195224", "SRS19251239", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 2", "GSM7854246", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 2", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854246", "GSM7854246: WT KM 2; Danio rerio; RNA Seq", "GSM7854246 r1", "GSM7854246", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "w2_S0_L003_R2_001.fastq.gz w2_S0_L003_R1_001.fastq.gz", "fastq fastq", 110520161400.0, 368400538.0, "GSM7854246 r1", "0:150 1:150", "A:44333853620;C:20994101993;G:19951597607;T:25238178463;N:2429717", 150, 150, null, null, 44333853620, 20994101993, 19951597607, 25238178463, 2429717, "SRX22195224", "SRS19251239", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.84344, 0.0, 0.0961, 1.0, 0.83485, null, 0.63275, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28607, "SRR26491387", "SRX22195223", "SRS19251238", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 1", "GSM7854245", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854245", "GSM7854245: WT KM 1; Danio rerio; RNA Seq", "GSM7854245 r1", "GSM7854245", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "WKM-WKM-1_BKDL190841222-1a-AK650_1.fq.gz WKM-WKM-1_BKDL190841222-1a-AK650_2.fq.gz", "fastq fastq", 20481536700.0, 68271789.0, "GSM7854245 r1", "0:150 1:150", "A:4681473958;C:3918612929;G:6623380714;T:5257792172;N:276927", 150, 150, null, null, 4681473958, 3918612929, 6623380714, 5257792172, 276927, "SRX22195223", "SRS19251238", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.91381, 0.0, 0.08281, 1.0, 0.82386, null, 0.55976, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28608, "SRR26491388", "SRX22195223", "SRS19251238", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 1", "GSM7854245", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854245", "GSM7854245: WT KM 1; Danio rerio; RNA Seq", "GSM7854245 r1", "GSM7854245", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "WKM-WKM-2_BKDL190841222-1a-AK651_2.fq.gz WKM-WKM-2_BKDL190841222-1a-AK651_1.fq.gz", "fastq fastq", 24824596500.0, 82748655.0, "GSM7854245 r2", "0:150 1:150", "A:5675288010;C:4753602834;G:8033499593;T:6361861422;N:344641", 150, 150, null, null, 5675288010, 4753602834, 8033499593, 6361861422, 344641, "SRX22195223", "SRS19251238", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.9121, 0.0, 0.08282, 1.0, 0.82613, null, 0.56378, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28609, "SRR26491389", "SRX22195223", "SRS19251238", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 1", "GSM7854245", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854245", "GSM7854245: WT KM 1; Danio rerio; RNA Seq", "GSM7854245 r1", "GSM7854245", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "WKM-WKM-3_BKDL190841222-1a-AK652_1.fq.gz WKM-WKM-3_BKDL190841222-1a-AK652_2.fq.gz", "fastq fastq", 20574633600.0, 68582112.0, "GSM7854245 r3", "0:150 1:150", "A:4698580031;C:3942306152;G:6657096764;T:5276366726;N:283927", 150, 150, null, null, 4698580031, 3942306152, 6657096764, 5276366726, 283927, "SRX22195223", "SRS19251238", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.9136, 0.0, 0.08366, 1.0, 0.82373, null, 0.55683, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28610, "SRR26491390", "SRX22195223", "SRS19251238", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 1", "GSM7854245", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854245", "GSM7854245: WT KM 1; Danio rerio; RNA Seq", "GSM7854245 r1", "GSM7854245", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "WKM-WKM-4_BKDL190841222-1a-AK653_2.fq.gz WKM-WKM-4_BKDL190841222-1a-AK653_1.fq.gz", "fastq fastq", 25381641600.0, 84605472.0, "GSM7854245 r4", "0:150 1:150", "A:5785664179;C:4874470993;G:8220023956;T:6501127037;N:355435", 150, 150, null, null, 5785664179, 4874470993, 8220023956, 6501127037, 355435, "SRX22195223", "SRS19251238", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.91371, 0.0, 0.08381, 1.0, 0.8244, null, 0.57179, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [33649, "SRR30353607", "SRX25811748", "SRS22442019", "SRP528282", "PRJNA1151637", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq]", "GSE275537", "Transcriptome Analysis", "Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells 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. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.", null, "pubmed:39548947", null, "Rad21het rep2", "GSM8479120", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep2", "Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes  features and matrix files", "Whole kidney marrow", null, "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479120", "GSM8479120: Rad21het rep2; Danio rerio; RNA Seq", "GSM8479120 r1", "GSM8479120", "1", "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP528282", null, null, "Rad21het_rep2_S1_L001_R2_001.fastq.gz Rad21het_rep2_S1_L001_R1_001.fastq.gz", "fastq fastq", 25307099168.0, 218164648.0, "GSM8479120 r1", "0:27 1:89", "A:6829044594;C:5976366733;G:6024781695;T:6476303884;N:602262", 27, 89, null, null, 6829044594, 5976366733, 6024781695, 6476303884, 602262, "SRX25811748", "SRS22442019", "SRA1954153", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.00381, 0.89166, 0.00123, 0.07968, 0.99279, 0.82956, 0.36032, 0.51023, 27, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33650, "SRR30353608", "SRX25811747", "SRS22442018", "SRP528282", "PRJNA1151637", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq]", "GSE275537", "Transcriptome Analysis", "Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells 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. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.", null, "pubmed:39548947", null, "Rad21het rep1", "GSM8479119", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep1", "Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes  features and matrix files", "Whole kidney marrow", null, "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479119", "GSM8479119: Rad21het rep1; Danio rerio; RNA Seq", "GSM8479119 r1", "GSM8479119", "1", "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP528282", null, null, "Rad21het_rep1_S1_L001_R2_001.fastq.gz Rad21het_rep1_S1_L001_R1_001.fastq.gz", "fastq fastq", 22413519188.0, 193219993.0, "GSM8479119 r1", "0:27 1:89", "A:6260052051;C:5058503439;G:5315821015;T:5778634222;N:508461", 27, 89, null, null, 6260052051, 5058503439, 5315821015, 5778634222, 508461, "SRX25811747", "SRS22442018", "SRA1954153", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.00394, 0.90508, 0.00119, 0.09071, 0.99162, 0.82942, 0.3619, 0.54526, 27, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33651, "SRR30353609", "SRX25811746", "SRS22442017", "SRP528282", "PRJNA1151637", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq]", "GSE275537", "Transcriptome Analysis", "Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells 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. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.", null, "pubmed:39548947", null, "WT rep2", "GSM8479118", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep2", "Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes  features and matrix files", "Whole kidney marrow", null, "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479118", "GSM8479118: WT rep2; Danio rerio; RNA Seq", "GSM8479118 r1", "GSM8479118", "1", "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP528282", null, null, "WT_rep2_S1_L001_R1_001.fastq.gz WT_rep2_S1_L001_R2_001.fastq.gz", "fastq fastq", 23457592964.0, 202220629.0, "GSM8479118 r1", "0:27 1:89", "A:6426793246;C:5417323760;G:5551103780;T:6061805923;N:566255", 27, 89, null, null, 6426793246, 5417323760, 5551103780, 6061805923, 566255, "SRX25811746", "SRS22442017", "SRA1954153", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.00406, 0.91487, 0.00142, 0.09007, 0.99283, 0.82641, 0.37549, 0.51858, 27, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33652, "SRR30353610", "SRX25811745", "SRS22442016", "SRP528282", "PRJNA1151637", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq]", "GSE275537", "Transcriptome Analysis", "Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells 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. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.", null, "pubmed:39548947", null, "WT rep1", "GSM8479117", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep1", "Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes  features and matrix files", "Whole kidney marrow", null, "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479117", "GSM8479117: WT rep1; Danio rerio; RNA Seq", "GSM8479117 r1", "GSM8479117", "1", "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP528282", null, null, "WT_rep1_S1_L001_R2_001.fastq.gz WT_rep1_S1_L001_R1_001.fastq.gz", "fastq fastq", 26909031908.0, 231974413.0, "GSM8479117 r1", "0:27 1:89", "A:7272478752;C:6312728360;G:6433038501;T:6890198195;N:588100", 27, 89, null, null, 7272478752, 6312728360, 6433038501, 6890198195, 588100, "SRX25811745", "SRS22442016", "SRA1954153", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.00366, 0.93902, 0.00134, 0.0858, 0.99318, 0.82769, 0.35, 0.51885, 27, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [70440, "SRR19859693", "SRX15903239", "SRS13591719", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  cmyb pu.1  replicate 1", "GSM6267523", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper;pu.1G242D/G242D", "km  cmyb pu.1  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper;pu.1G242D/G242D", "GSM6267523", "GSM6267523: km  cmyb pu.1  replicate 1; Danio rerio; RNA Seq", "GSM6267523 r1", "GSM6267523", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "CMYB-PU1_S1_L001_R1_001.fastq.gz CMYB-PU1_S1_L001_R2_001.fastq.gz", "fastq fastq", 34019964900.0, 113399883.0, "GSM6267523 r1", "0:150 1:150", "A:13302713965;C:6219483502;G:5997466590;T:8499713816;N:587027", 150, 150, null, null, 13302713965, 6219483502, 5997466590, 8499713816, 587027, "SRX15903239", "SRS13591719", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.91115, 0.0, 0.08658, 1.0, 0.8309, null, 0.54286, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70441, "SRR19859694", "SRX15903239", "SRS13591719", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  cmyb pu.1  replicate 1", "GSM6267523", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper;pu.1G242D/G242D", "km  cmyb pu.1  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper;pu.1G242D/G242D", "GSM6267523", "GSM6267523: km  cmyb pu.1  replicate 1; Danio rerio; RNA Seq", "GSM6267523 r1", "GSM6267523", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "CMYB-PU1_S1_L002_R1_001.fastq.gz CMYB-PU1_S1_L002_R2_001.fastq.gz", "fastq fastq", 35297063100.0, 117656877.0, "GSM6267523 r2", "0:150 1:150", "A:13842297260;C:6470166563;G:6221506653;T:8762475764;N:616860", 150, 150, null, null, 13842297260, 6470166563, 6221506653, 8762475764, 616860, "SRX15903239", "SRS13591719", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.90973, 0.0, 0.08598, 1.0, 0.83207, null, 0.53444, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70442, "SRR19859695", "SRX15903239", "SRS13591719", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  cmyb pu.1  replicate 1", "GSM6267523", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper;pu.1G242D/G242D", "km  cmyb pu.1  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper;pu.1G242D/G242D", "GSM6267523", "GSM6267523: km  cmyb pu.1  replicate 1; Danio rerio; RNA Seq", "GSM6267523 r1", "GSM6267523", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "CMYB-PU1_S1_L003_R1_001.fastq.gz CMYB-PU1_S1_L003_R2_001.fastq.gz", "fastq fastq", 39539379300.0, 131797931.0, "GSM6267523 r3", "0:150 1:150", "A:15520523231;C:7246463770;G:6961630911;T:9810076786;N:684602", 150, 150, null, null, 15520523231, 7246463770, 6961630911, 9810076786, 684602, "SRX15903239", "SRS13591719", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.90947, 0.0, 0.08463, 1.0, 0.8324, null, 0.53674, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70443, "SRR19859696", "SRX15903239", "SRS13591719", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  cmyb pu.1  replicate 1", "GSM6267523", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper;pu.1G242D/G242D", "km  cmyb pu.1  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper;pu.1G242D/G242D", "GSM6267523", "GSM6267523: km  cmyb pu.1  replicate 1; Danio rerio; RNA Seq", "GSM6267523 r1", "GSM6267523", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "CMYB-PU1_S1_L004_R1_001.fastq.gz CMYB-PU1_S1_L004_R2_001.fastq.gz", "fastq fastq", 27237789000.0, 90792630.0, "GSM6267523 r4", "0:150 1:150", "A:10681142634;C:4985008024;G:4794135810;T:6777034408;N:468124", 150, 150, null, null, 10681142634, 4985008024, 4794135810, 6777034408, 468124, "SRX15903239", "SRS13591719", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.90965, 0.0, 0.08455, 1.0, 0.83323, null, 0.52704, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70444, "SRR19859697", "SRX15903238", "SRS13591718", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  pu.1  replicate 1", "GSM6267522", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:pu.1G242D/G242D", "km  pu.1  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:pu.1G242D/G242D", "GSM6267522", "GSM6267522: km  pu.1  replicate 1; Danio rerio; RNA Seq", "GSM6267522 r1", "GSM6267522", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "PU1_S1_L001_R2_001.fastq.gz PU1_S1_L001_R1_001.fastq.gz", "fastq fastq", 30561360600.0, 101871202.0, "GSM6267522 r1", "0:150 1:150", "A:11906530728;C:5697892695;G:5454406722;T:7501998919;N:531536", 150, 150, null, null, 11906530728, 5697892695, 5454406722, 7501998919, 531536, "SRX15903238", "SRS13591718", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.92267, 0.0, 0.08125, 1.0, 0.83059, null, 0.51501, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70445, "SRR19859698", "SRX15903238", "SRS13591718", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  pu.1  replicate 1", "GSM6267522", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:pu.1G242D/G242D", "km  pu.1  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:pu.1G242D/G242D", "GSM6267522", "GSM6267522: km  pu.1  replicate 1; Danio rerio; RNA Seq", "GSM6267522 r1", "GSM6267522", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "PU1_S1_L002_R2_001.fastq.gz PU1_S1_L002_R1_001.fastq.gz", "fastq fastq", 31673039700.0, 105576799.0, "GSM6267522 r2", "0:150 1:150", "A:12352655582;C:5907788344;G:5644796332;T:7767253658;N:545784", 150, 150, null, null, 12352655582, 5907788344, 5644796332, 7767253658, 545784, "SRX15903238", "SRS13591718", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.92309, 0.0, 0.08057, 1.0, 0.82984, null, 0.50946, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70446, "SRR19859699", "SRX15903238", "SRS13591718", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  pu.1  replicate 1", "GSM6267522", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:pu.1G242D/G242D", "km  pu.1  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:pu.1G242D/G242D", "GSM6267522", "GSM6267522: km  pu.1  replicate 1; Danio rerio; RNA Seq", "GSM6267522 r1", "GSM6267522", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "PU1_S1_L003_R2_001.fastq.gz PU1_S1_L003_R1_001.fastq.gz", "fastq fastq", 33526359900.0, 111754533.0, "GSM6267522 r3", "0:150 1:150", "A:13068066959;C:6255819442;G:5984040376;T:8217848342;N:584781", 150, 150, null, null, 13068066959, 6255819442, 5984040376, 8217848342, 584781, "SRX15903238", "SRS13591718", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.92206, 0.0, 0.08091, 1.0, 0.82974, null, 0.51636, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70447, "SRR19859700", "SRX15903238", "SRS13591718", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  pu.1  replicate 1", "GSM6267522", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:pu.1G242D/G242D", "km  pu.1  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:pu.1G242D/G242D", "GSM6267522", "GSM6267522: km  pu.1  replicate 1; Danio rerio; RNA Seq", "GSM6267522 r1", "GSM6267522", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "PU1_S1_L004_R2_001.fastq.gz PU1_S1_L004_R1_001.fastq.gz", "fastq fastq", 30888609300.0, 102962031.0, "GSM6267522 r4", "0:150 1:150", "A:12051215492;C:5766436866;G:5509059578;T:7561366493;N:530871", 150, 150, null, null, 12051215492, 5766436866, 5509059578, 7561366493, 530871, "SRX15903238", "SRS13591718", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.92394, 0.0, 0.08207, 1.0, 0.83073, null, 0.52682, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70448, "SRR19859701", "SRX15903237", "SRS13591717", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  cmyb  replicate 1", "GSM6267521", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper", "km  cmyb  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper", "GSM6267521", "GSM6267521: km  cmyb  replicate 1; Danio rerio; RNA Seq", "GSM6267521 r1", "GSM6267521", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "CMYB_S1_L001_R1_001.fastq.gz CMYB_S1_L001_R2_001.fastq.gz", "fastq fastq", 34497616200.0, 114992054.0, "GSM6267521 r1", "0:150 1:150", "A:13504826777;C:6266297436;G:6074966025;T:8650924155;N:601807", 150, 150, null, null, 13504826777, 6266297436, 6074966025, 8650924155, 601807, "SRX15903237", "SRS13591717", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.91763, 0.0, 0.08321, 1.0, 0.82824, null, 0.5179, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70449, "SRR19859702", "SRX15903237", "SRS13591717", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  cmyb  replicate 1", "GSM6267521", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper", "km  cmyb  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper", "GSM6267521", "GSM6267521: km  cmyb  replicate 1; Danio rerio; RNA Seq", "GSM6267521 r1", "GSM6267521", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "CMYB_S1_L002_R1_001.fastq.gz CMYB_S1_L002_R2_001.fastq.gz", "fastq fastq", 28088506500.0, 93628355.0, "GSM6267521 r2", "0:150 1:150", "A:11015834088;C:5102428324;G:4940837753;T:7028920003;N:486332", 150, 150, null, null, 11015834088, 5102428324, 4940837753, 7028920003, 486332, "SRX15903237", "SRS13591717", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.91409, 0.0, 0.08259, 1.0, 0.83011, null, 0.52084, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70450, "SRR19859703", "SRX15903237", "SRS13591717", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  cmyb  replicate 1", "GSM6267521", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper", "km  cmyb  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper", "GSM6267521", "GSM6267521: km  cmyb  replicate 1; Danio rerio; RNA Seq", "GSM6267521 r1", "GSM6267521", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "CMYB_S1_L003_R1_001.fastq.gz CMYB_S1_L003_R2_001.fastq.gz", "fastq fastq", 36358986600.0, 121196622.0, "GSM6267521 r3", "0:150 1:150", "A:14265106920;C:6611499551;G:6398314454;T:9083430714;N:634961", 150, 150, null, null, 14265106920, 6611499551, 6398314454, 9083430714, 634961, "SRX15903237", "SRS13591717", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.9165, 0.0, 0.08378, 1.0, 0.82938, null, 0.51904, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70451, "SRR19859704", "SRX15903237", "SRS13591717", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  cmyb  replicate 1", "GSM6267521", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper", "km  cmyb  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:cmybhyper", "GSM6267521", "GSM6267521: km  cmyb  replicate 1; Danio rerio; RNA Seq", "GSM6267521 r1", "GSM6267521", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "CMYB_S1_L004_R1_001.fastq.gz CMYB_S1_L004_R2_001.fastq.gz", "fastq fastq", 27447570900.0, 91491903.0, "GSM6267521 r4", "0:150 1:150", "A:10742787251;C:4983787095;G:4834284966;T:6886254319;N:457269", 150, 150, null, null, 10742787251, 4983787095, 4834284966, 6886254319, 457269, "SRX15903237", "SRS13591717", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.91673, 0.0, 0.08347, 1.0, 0.82779, null, 0.51722, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70452, "SRR19859705", "SRX15903236", "SRS13591716", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  wildtype  replicate 1", "GSM6267520", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:wt", "km  wildtype  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:wt", "GSM6267520", "GSM6267520: km  wildtype  replicate 1; Danio rerio; RNA Seq", "GSM6267520 r1", "GSM6267520", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "wildtype_S1_L001_R2_001.fastq.gz wildtype_S1_L001_R1_001.fastq.gz", "fastq fastq", 27770111700.0, 92567039.0, "GSM6267520 r1", "0:150 1:150", "A:10654881712;C:5315111692;G:4977483030;T:6822156857;N:478409", 150, 150, null, null, 10654881712, 5315111692, 4977483030, 6822156857, 478409, "SRX15903236", "SRS13591716", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.90999, 0.0, 0.06416, 1.0, 0.83909, null, 0.46343, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70453, "SRR19859706", "SRX15903236", "SRS13591716", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  wildtype  replicate 1", "GSM6267520", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:wt", "km  wildtype  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:wt", "GSM6267520", "GSM6267520: km  wildtype  replicate 1; Danio rerio; RNA Seq", "GSM6267520 r1", "GSM6267520", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "wildtype_S1_L002_R1_001.fastq.gz wildtype_S1_L002_R2_001.fastq.gz", "fastq fastq", 28400815500.0, 94669385.0, "GSM6267520 r2", "0:150 1:150", "A:10873206022;C:5429493184;G:5098301047;T:6999325016;N:490231", 150, 150, null, null, 10873206022, 5429493184, 5098301047, 6999325016, 490231, "SRX15903236", "SRS13591716", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.90904, 0.0, 0.06513, 1.0, 0.83974, null, 0.47032, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70454, "SRR19859707", "SRX15903236", "SRS13591716", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  wildtype  replicate 1", "GSM6267520", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:wt", "km  wildtype  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:wt", "GSM6267520", "GSM6267520: km  wildtype  replicate 1; Danio rerio; RNA Seq", "GSM6267520 r1", "GSM6267520", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "wildtype_S1_L003_R1_001.fastq.gz wildtype_S1_L003_R2_001.fastq.gz", "fastq fastq", 28329104400.0, 94430348.0, "GSM6267520 r3", "0:150 1:150", "A:10825269916;C:5409383714;G:5088945275;T:7005019444;N:486051", 150, 150, null, null, 10825269916, 5409383714, 5088945275, 7005019444, 486051, "SRX15903236", "SRS13591716", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.90932, 0.0, 0.06506, 1.0, 0.83909, null, 0.47011, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [70455, "SRR19859708", "SRX15903236", "SRS13591716", "SRP383719", "PRJNA853194", "The synergistic effect of c Myb hyperactivation and Pu.1 deficiency in inducing Pelger Hu\u00ebt anomaly and promoting sAML transformation", "GSE206979", "Transcriptome Analysis", "Patients with acute myeloid leukemia developed from myelodysplastic syndrome MDS/AML have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes  including co occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However  the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study  we used the c Myb hyperactivation and Pu.1 deficient double strain c mybhyper;pu.1G242D/G242D zebrafish to clarify the synergistic role of c Myb and Pu.1 in promoting MDS/AML development. We found that the c mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils  and progressed to MDS/AML with a high ratio. Interestingly  a group of poorly differentiated Pelger Hu\u00ebt like neutrophils was identified in c mybhyper;pu.1G242D/G242D maturity and might be associated with MDS/AML progression. Moreover  treated the c mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine Ara C and the differential inducer all trans retinoic acid ATRA could effectively relieve the leukemic symptoms. Our findings revealed that c Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore  c mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening. Overall design: Kidney marrow of the wildtype  c mybhyper  pu.1G242D/G242D  c mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:40020188", null, "km  wildtype  replicate 1", "GSM6267520", null, "source name:kidney marrow|development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:wt", "km  wildtype  replicate 1", "10X Genomics Cell Ranger software version 3.1.0 was used to convert raw BCL files to FASTQ files  alignment and counts quantification. Doublet GEMs was achieved by using the tool DoubletFinder v2.0.3 by the generation of artificial doublets  using the PC distance to find each cell\u2019s proportion of artificial k nearest neighbors pANN and ranking them according to the expected number of doublets The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs \u226540000 or mitochondrial gene percent \u226515% were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected. post removing unwanted cells from the dataset  we employed a global scaling normalization method \u201cLogNormalize\u201d that normalizes the gene expression measurements for each cell by the total expression  multiplies this by a scale factor 10 000 by default  and log transforms the results. Seurat embed cells in a shared nearest neighbor SNN graph  with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi cliques or communities  we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods Jaccard distance. We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters  t distributed Stochastic Neighbor Embedding t SNE were generated using the same PCs. Assembly: GRCz11 Ensembl release 100 Supplementary files format and content: tab separated values files  matrix files", "kidney marrow", null, "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3\u2019 Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "development stage:1 year old|tissue:kidney marrow|cell type:blood cells|genotype:wt", "GSM6267520", "GSM6267520: km  wildtype  replicate 1; Danio rerio; RNA Seq", "GSM6267520 r1", "GSM6267520", "1", "Kidney marrow were isolated from 1 year old fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was \u226590%  the cell concentration was adjusted to 1 000 cells/\u03bcL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Briefly  blood cell suspensions were loaded on a 10X Genomics GemCode Single cell instrument to generates single cell Gel Bead In EMlusion GEMs. Upon dissolution of the Gel Bead in a GEM  primers containing an Illumina\u00ae R1 sequence  a 16 nt 10x Barcode  a 10 nt Unique Molecular Identifier UMI  and a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads  amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383719", null, null, "wildtype_S1_L004_R1_001.fastq.gz wildtype_S1_L004_R2_001.fastq.gz", "fastq fastq", 27767976900.0, 92559923.0, "GSM6267520 r4", "0:150 1:150", "A:10620981494;C:5311554239;G:4991425527;T:6843535693;N:479947", 150, 150, null, null, 10620981494, 5311554239, 4991425527, 6843535693, 479947, "SRX15903236", "SRS13591716", "SRA1444282", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.0, 0.90991, 0.0, 0.06382, 1.0, 0.83814, null, 0.46543, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-06-27", "Adult", "Adult", "Kidney", "Renal System"], [74455, "SRR23804140", "SRX19635460", "SRS17004492", "SRP426651", "PRJNA943248", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]", "GSE227115", "Transcriptome Analysis", "We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected  homogenized  filtered  and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "kdrl:GFP+  adult kidney", "GSM7091842", null, "source name:kdrl:GFP transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney", "kdrl:GFP+  adult kidney", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "kdrl:GFP transgenic zebrafish adult kidney wild type", "No treatments", "Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer.  Adult kidneys were dissected then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.", "developmental stage:adult|genotype:wild type|tissue:kidney", "GSM7091842", "GSM7091842: kdrl:GFP+  adult kidney; Danio rerio; RNA Seq", "GSM7091842 r1", "GSM7091842", "1", "Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426651", null, null, "FLK-G_Single_Cell_ACTCTAGG.fastq.sorted.fastq.gz", "fastq", 10648313404.0, 80407702.0, "GSM7091842 r1", "0:132.43", "A:3393628100;C:2087372845;G:1953079760;T:3213786135;N:446564", 132, null, null, null, 3393628100, 2087372845, 1953079760, 3213786135, 446564, "SRX19635460", "SRS17004492", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.60891, null, 0.10525, null, 0.81903, null, 0.52577, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Adult", "Adult", "Kidney", "Renal System"], [74456, "SRR23804141", "SRX19635459", "SRS17004491", "SRP426651", "PRJNA943248", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]", "GSE227115", "Transcriptome Analysis", "We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected  homogenized  filtered  and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "kdrl:mCherry+  adult kidney  rep2", "GSM7091841", null, "source name:kdrl:mCherry transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney", "kdrl:mCherry+  adult kidney  rep2", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "kdrl:mCherry transgenic zebrafish adult kidney wild type", "No treatments", "Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer.  Adult kidneys were dissected then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.", "developmental stage:adult|genotype:wild type|tissue:kidney", "GSM7091841", "GSM7091841: kdrl:mCherry+  adult kidney  rep2; Danio rerio; RNA Seq", "GSM7091841 r1", "GSM7091841", "1", "Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426651", null, null, "FLK-R_Single_Cell_CTAGTCGA.fastq.sorted.fastq.gz", "fastq", 13922952441.0, 105098464.0, "GSM7091841 r1", "0:132.48", "A:4341235438;C:2807868369;G:2579519980;T:4193742000;N:586654", 132, null, null, null, 4341235438, 2807868369, 2579519980, 4193742000, 586654, "SRX19635459", "SRS17004491", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.64512, null, 0.12315, null, 0.81712, null, 0.52922, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Adult", "Adult", "Kidney", "Renal System"], [74457, "SRR23804142", "SRX19635458", "SRS17004490", "SRP426651", "PRJNA943248", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney]", "GSE227115", "Transcriptome Analysis", "We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected  homogenized  filtered  and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "kdrl:mCherry+  adult kidney  rep1", "GSM7091840", null, "source name:kdrl:mCherry transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney", "kdrl:mCherry+  adult kidney  rep1", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "kdrl:mCherry transgenic zebrafish adult kidney wild type", "No treatments", "Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer.  Adult kidneys were dissected then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.", "developmental stage:adult|genotype:wild type|tissue:kidney", "GSM7091840", "GSM7091840: kdrl:mCherry+  adult kidney  rep1; Danio rerio; RNA Seq", "GSM7091840 r1", "GSM7091840", "1", "Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426651", null, null, "KLR_Single_Cell_ATTAGACG.fastq.sorted.fastq.gz", "fastq", 8774502682.0, 64692571.0, "GSM7091840 r1", "0:135.63", "A:2791773089;C:1725088037;G:1633088372;T:2624197073;N:356111", 135, null, null, null, 2791773089, 1725088037, 1633088372, 2624197073, 356111, "SRX19635458", "SRS17004490", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.66981, null, 0.10372, null, 0.81357, null, 0.5394, null, 38, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Adult", "Adult", "Kidney", "Renal System"]], "truncated": false, "filtered_table_rows_count": 52, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_source\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC SINGLE CELL", "p1": "Kidney"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Kidney", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 52, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Kidney&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Kidney", "results": [{"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 52, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Kidney", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Kidney", "results": [{"value": "cDNA", "label": "cDNA", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Kidney&experiment.library_selection=cDNA", "selected": false}, {"value": "PolyA", "label": "PolyA", 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