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
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,,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,,,,,,,,,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,,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,,,,7555470312,5144518052,5682746714,6882396490,1305628,ERX5471113,ERS6291553,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.90876,,0.18424,,0.84017,,0.55508,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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,,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,,,,10397161431,8128518427,8799445454,9049686061,1896722,ERX5471112,ERS6291552,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.94708,,0.08938,,0.85449,,0.52917,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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,,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,,,,6732382430,4540586585,4933684272,6209137814,1096301,ERX5471111,ERS6291551,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.91306,,0.21566,,0.83469,,0.53782,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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,,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,,,,,,,,,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,,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,,,,5232521408,3876317502,4287902596,4606191653,1357600,ERX5471110,ERS6291550,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.94131,,0.08871,,0.83465,,0.52792,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:38497789,,vaccinated+SVCV  scRNAseq Kidney leukocyte,GSM7749529,,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,,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 μm 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 μg/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 3’ 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.,,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 μm 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 μg/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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP457977,,,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,,,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,,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.,,pubmed:38497789,,SVCV  scRNAseq Kidney leukocyte,GSM7749528,,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,,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 μm 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 μg/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 3’ 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.,,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 μm 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 μg/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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP457977,,,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,,,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,,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.,,pubmed:38497789,,PBS  scRNAseq Kidney leukocyte,GSM7749527,,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,,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 μm 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 μg/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 3’ 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.,,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 μm 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 μg/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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP457977,,,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,,,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,,China,2023-09-01,Juvenile,Juvenile,Kidney,Renal System
28589,SRR26491369,SRX22195232,SRS19251247,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,KM eos,GSM7854254,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28590,SRR26491370,SRX22195232,SRS19251247,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,KM eos,GSM7854254,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28591,SRR26491371,SRX22195232,SRS19251247,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,KM eos,GSM7854254,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28592,SRR26491372,SRX22195232,SRS19251247,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,KM eos,GSM7854254,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28593,SRR26491373,SRX22195231,SRS19251246,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebpb mut KM 3,GSM7854253,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,0.69315,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28594,SRR26491374,SRX22195230,SRS19251245,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebpb mut KM 2,GSM7854252,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,0.631,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28595,SRR26491375,SRX22195229,SRS19251244,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebpb mut KM 1,GSM7854251,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28596,SRR26491376,SRX22195229,SRS19251244,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebpb mut KM 1,GSM7854251,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28597,SRR26491377,SRX22195229,SRS19251244,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebpb mut KM 1,GSM7854251,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28598,SRR26491378,SRX22195229,SRS19251244,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebpb mut KM 1,GSM7854251,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28599,SRR26491379,SRX22195228,SRS19251243,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebp1 mut KM 3,GSM7854250,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,0.55652,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28600,SRR26491380,SRX22195227,SRS19251242,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebp1 mut KM 2,GSM7854249,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,0.5598,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28601,SRR26491381,SRX22195226,SRS19251241,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebp1 mut KM 1,GSM7854248,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,0.5956,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28602,SRR26491382,SRX22195226,SRS19251241,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebp1 mut KM 1,GSM7854248,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,0.60651,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28603,SRR26491383,SRX22195226,SRS19251241,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebp1 mut KM 1,GSM7854248,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,0.57797,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28604,SRR26491384,SRX22195226,SRS19251241,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,cebp1 mut KM 1,GSM7854248,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,0.59712,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28605,SRR26491385,SRX22195225,SRS19251240,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,WT KM 3,GSM7854247,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,0.64916,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28606,SRR26491386,SRX22195224,SRS19251239,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,WT KM 2,GSM7854246,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,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,,,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,,0.63275,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28607,SRR26491387,SRX22195223,SRS19251238,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,WT KM 1,GSM7854245,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,0.55976,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28608,SRR26491388,SRX22195223,SRS19251238,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,WT KM 1,GSM7854245,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,0.56378,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28609,SRR26491389,SRX22195223,SRS19251238,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,WT KM 1,GSM7854245,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,0.55683,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-10-23,Adult,Adult,Kidney,Renal System
28610,SRR26491390,SRX22195223,SRS19251238,SRP468071,PRJNA1031138,Cebp1 and Cebpß 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 Cebpß 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,,WT KM 1,GSM7854245,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP468071,,,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,,,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,,0.57179,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:39548947,,Rad21het rep2,GSM8479120,,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,,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 µm 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′ GEM library and Gel bead Kit v3.1 10x Genomics.,,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 µm 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′ GEM library and Gel bead Kit v3.1 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP528282,,,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,,,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,,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.,,pubmed:39548947,,Rad21het rep1,GSM8479119,,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,,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 µm 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′ GEM library and Gel bead Kit v3.1 10x Genomics.,,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 µm 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′ GEM library and Gel bead Kit v3.1 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP528282,,,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,,,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,,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.,,pubmed:39548947,,WT rep2,GSM8479118,,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,,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 µm 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′ GEM library and Gel bead Kit v3.1 10x Genomics.,,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 µm 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′ GEM library and Gel bead Kit v3.1 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP528282,,,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,,,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,,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.,,pubmed:39548947,,WT rep1,GSM8479117,,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,,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 µm 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′ GEM library and Gel bead Kit v3.1 10x Genomics.,,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 µm 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′ GEM library and Gel bead Kit v3.1 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP528282,,,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,,,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,,New Zealand,2024-08-23,Adult,Adult,Kidney,Renal System
64483,SRR14713035,SRX11050991,SRS9118959,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 heterozygous [het2],GSM5353444,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,runx1 heterozygous [het2],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,GSM5353444,GSM5353444: runx1 heterozygous [het2]; Danio rerio; RNA Seq,GSM5353444,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353444,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=het2 S3 L001 I1 001.fastq.gz   read2PairFiles=het2 S3 L001 R1 001.fastq.gz   read3PairFiles=het2 S3 L001 R2 001.fastq.gz,het2_S3_L001_I1_001.fastq.gz het2_S3_L001_R1_001.fastq.gz het2_S3_L001_R2_001.fastq.gz,fastq fastq fastq,15663557054.0,124177953.0,GSM5353444 r1,0:8 1:27.58 2:90.56,A:3222090217;C:2457731774;G:2657226801;T:2906730616;N:1348005,8,27,90,,3222090217,2457731774,2657226801,2906730616,1348005,SRX11050991,SRS9118959,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.93627,,0.12855,,0.80722,,0.53604,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64484,SRR14713036,SRX11050991,SRS9118959,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 heterozygous [het2],GSM5353444,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,runx1 heterozygous [het2],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,GSM5353444,GSM5353444: runx1 heterozygous [het2]; Danio rerio; RNA Seq,GSM5353444,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353444,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=het2 S3 L002 I1 001.fastq.gz   read2PairFiles=het2 S3 L002 R1 001.fastq.gz   read3PairFiles=het2 S3 L002 R2 001.fastq.gz,het2_S3_L002_I1_001.fastq.gz het2_S3_L002_R1_001.fastq.gz het2_S3_L002_R2_001.fastq.gz,fastq fastq fastq,15733917976.0,124735364.0,GSM5353444 r2,0:8 1:27.58 2:90.56,A:3236625131;C:2468696674;G:2669813570;T:2919169352;N:1355273,8,27,90,,3236625131,2468696674,2669813570,2919169352,1355273,SRX11050991,SRS9118959,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.93597,,0.12775,,0.80872,,0.52945,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64485,SRR14713033,SRX11050990,SRS9118958,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 heterozygous [het1],GSM5353443,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,runx1 heterozygous [het1],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,GSM5353443,GSM5353443: runx1 heterozygous [het1]; Danio rerio; RNA Seq,GSM5353443,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353443,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=het1 S1 L001 I1 001.fastq.gz   read2PairFiles=het1 S1 L001 R1 001.fastq.gz   read3PairFiles=het1 S1 L001 R2 001.fastq.gz,het1_S1_L001_I1_001.fastq.gz het1_S1_L001_R1_001.fastq.gz het1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,14144386609.0,112134541.0,GSM5353443 r1,0:8 1:27.58 2:90.56,A:2911415156;C:2232516450;G:2400128566;T:2609309040;N:1216894,8,27,90,,2911415156,2232516450,2400128566,2609309040,1216894,SRX11050990,SRS9118958,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.93943,,0.1263,,0.81055,,0.54188,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64486,SRR14713034,SRX11050990,SRS9118958,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 heterozygous [het1],GSM5353443,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,runx1 heterozygous [het1],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,GSM5353443,GSM5353443: runx1 heterozygous [het1]; Danio rerio; RNA Seq,GSM5353443,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353443,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=het1 S1 L002 I1 001.fastq.gz   read2PairFiles=het1 S1 L002 R1 001.fastq.gz   read3PairFiles=het1 S1 L002 R2 001.fastq.gz,het1_S1_L002_I1_001.fastq.gz het1_S1_L002_R1_001.fastq.gz het1_S1_L002_R2_001.fastq.gz,fastq fastq fastq,14198963993.0,112567012.0,GSM5353443 r2,0:8 1:27.58 2:90.56,A:2922564124;C:2241222197;G:2410043722;T:2618704172;N:1244941,8,27,90,,2922564124,2241222197,2410043722,2618704172,1244941,SRX11050990,SRS9118958,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.93945,,0.1279,,0.81205,,0.54199,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64487,SRR14713047,SRX11050989,SRS9118957,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 homozygous [ko4],GSM5353450,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,runx1 homozygous [ko4],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,GSM5353450,GSM5353450: runx1 homozygous [ko4]; Danio rerio; RNA Seq,GSM5353450,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353450,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ko4 S8 L001 I1 001.fastq.gz   read2PairFiles=ko4 S8 L001 R1 001.fastq.gz   read3PairFiles=ko4 S8 L001 R2 001.fastq.gz,ko4_S8_L001_I1_001.fastq.gz ko4_S8_L001_R1_001.fastq.gz ko4_S8_L001_R2_001.fastq.gz,fastq fastq fastq,13992524630.0,110906152.0,GSM5353450 r1,0:8 1:27.58 2:90.58,A:2982262991;C:2094207271;G:2250607795;T:2718018274;N:1209671,8,27,90,,2982262991,2094207271,2250607795,2718018274,1209671,SRX11050989,SRS9118957,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.91453,,0.21027,,0.7724,,0.60148,,88,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64488,SRR14713048,SRX11050989,SRS9118957,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 homozygous [ko4],GSM5353450,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,runx1 homozygous [ko4],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,GSM5353450,GSM5353450: runx1 homozygous [ko4]; Danio rerio; RNA Seq,GSM5353450,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353450,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ko4 S8 L002 I1 001.fastq.gz   read2PairFiles=ko4 S8 L002 R1 001.fastq.gz   read3PairFiles=ko4 S8 L002 R2 001.fastq.gz,ko4_S8_L002_I1_001.fastq.gz ko4_S8_L002_R1_001.fastq.gz ko4_S8_L002_R2_001.fastq.gz,fastq fastq fastq,14045176738.0,111323195.0,GSM5353450 r2,0:8 1:27.58 2:90.58,A:2993422870;C:2102123853;G:2259649775;T:2727701329;N:1220191,8,27,90,,2993422870,2102123853,2259649775,2727701329,1220191,SRX11050989,SRS9118957,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.91368,,0.21103,,0.77305,,0.57218,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64489,SRR14713045,SRX11050988,SRS9118956,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 homozygous [ko3],GSM5353449,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,runx1 homozygous [ko3],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,GSM5353449,GSM5353449: runx1 homozygous [ko3]; Danio rerio; RNA Seq,GSM5353449,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353449,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ko3 S6 L001 I1 001.fastq.gz   read2PairFiles=ko3 S6 L001 R1 001.fastq.gz   read3PairFiles=ko3 S6 L001 R2 001.fastq.gz,ko3_S6_L001_I1_001.fastq.gz ko3_S6_L001_R1_001.fastq.gz ko3_S6_L001_R2_001.fastq.gz,fastq fastq fastq,18568439982.0,147229230.0,GSM5353449 r1,0:8 1:27.58 2:90.54,A:3724341578;C:3019598344;G:3052550431;T:3531772926;N:1597889,8,27,90,,3724341578,3019598344,3052550431,3531772926,1597889,SRX11050988,SRS9118956,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.94548,,0.14556,,0.80939,,0.56646,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64490,SRR14713046,SRX11050988,SRS9118956,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 homozygous [ko3],GSM5353449,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,runx1 homozygous [ko3],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,GSM5353449,GSM5353449: runx1 homozygous [ko3]; Danio rerio; RNA Seq,GSM5353449,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353449,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ko3 S6 L002 I1 001.fastq.gz   read2PairFiles=ko3 S6 L002 R1 001.fastq.gz   read3PairFiles=ko3 S6 L002 R2 001.fastq.gz,ko3_S6_L002_I1_001.fastq.gz ko3_S6_L002_R1_001.fastq.gz ko3_S6_L002_R2_001.fastq.gz,fastq fastq fastq,18641428578.0,147807474.0,GSM5353449 r2,0:8 1:27.58 2:90.54,A:3738835103;C:3031462473;G:3065268246;T:3545053140;N:1634465,8,27,90,,3738835103,3031462473,3065268246,3545053140,1634465,SRX11050988,SRS9118956,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.94636,,0.1465,,0.80872,,0.56839,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64491,SRR14713043,SRX11050987,SRS9118955,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 homozygous [ko2],GSM5353448,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,runx1 homozygous [ko2],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,GSM5353448,GSM5353448: runx1 homozygous [ko2]; Danio rerio; RNA Seq,GSM5353448,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353448,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ko2 S4 L001 I1 001.fastq.gz   read2PairFiles=ko2 S4 L001 R1 001.fastq.gz   read3PairFiles=ko2 S4 L001 R2 001.fastq.gz,ko2_S4_L001_I1_001.fastq.gz ko2_S4_L001_R1_001.fastq.gz ko2_S4_L001_R2_001.fastq.gz,fastq fastq fastq,13583701065.0,107729773.0,GSM5353448 r1,0:8 1:27.58 2:90.51,A:2614328803;C:2312765627;G:2286840395;T:2535315224;N:1170326,8,27,90,,2614328803,2312765627,2286840395,2535315224,1170326,SRX11050987,SRS9118955,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.9521,,0.10164,,0.83282,,0.53497,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64492,SRR14713044,SRX11050987,SRS9118955,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 homozygous [ko2],GSM5353448,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,runx1 homozygous [ko2],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,GSM5353448,GSM5353448: runx1 homozygous [ko2]; Danio rerio; RNA Seq,GSM5353448,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353448,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ko2 S4 L002 I1 001.fastq.gz   read2PairFiles=ko2 S4 L002 R1 001.fastq.gz   read3PairFiles=ko2 S4 L002 R2 001.fastq.gz,ko2_S4_L002_I1_001.fastq.gz ko2_S4_L002_R1_001.fastq.gz ko2_S4_L002_R2_001.fastq.gz,fastq fastq fastq,13638926054.0,108167655.0,GSM5353448 r2,0:8 1:27.58 2:90.51,A:2624803921;C:2322432212;G:2296753639;T:2544868462;N:1185166,8,27,90,,2624803921,2322432212,2296753639,2544868462,1185166,SRX11050987,SRS9118955,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.9514,,0.10219,,0.83402,,0.52448,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64493,SRR14713041,SRX11050986,SRS9118954,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 homozygous [ko1],GSM5353447,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,runx1 homozygous [ko1],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,GSM5353447,GSM5353447: runx1 homozygous [ko1]; Danio rerio; RNA Seq,GSM5353447,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353447,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ko1 S2 L001 I1 001.fastq.gz   read2PairFiles=ko1 S2 L001 R1 001.fastq.gz   read3PairFiles=ko1 S2 L001 R2 001.fastq.gz,ko1_S2_L001_I1_001.fastq.gz ko1_S2_L001_R1_001.fastq.gz ko1_S2_L001_R2_001.fastq.gz,fastq fastq fastq,13413711982.0,106340120.0,GSM5353447 r1,0:8 1:27.58 2:90.56,A:2784868205;C:2152619974;G:2140694771;T:2550343959;N:1164507,8,27,90,,2784868205,2152619974,2140694771,2550343959,1164507,SRX11050986,SRS9118954,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.94101,,0.13573,,0.80452,,0.63043,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64494,SRR14713042,SRX11050986,SRS9118954,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 homozygous [ko1],GSM5353447,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,runx1 homozygous [ko1],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 homozygous,GSM5353447,GSM5353447: runx1 homozygous [ko1]; Danio rerio; RNA Seq,GSM5353447,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353447,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ko1 S2 L002 I1 001.fastq.gz   read2PairFiles=ko1 S2 L002 R1 001.fastq.gz   read3PairFiles=ko1 S2 L002 R2 001.fastq.gz,ko1_S2_L002_I1_001.fastq.gz ko1_S2_L002_R1_001.fastq.gz ko1_S2_L002_R2_001.fastq.gz,fastq fastq fastq,13469390045.0,106781267.0,GSM5353447 r2,0:8 1:27.58 2:90.56,A:2796457564;C:2161673052;G:2149962960;T:2560388359;N:1176283,8,27,90,,2796457564,2161673052,2149962960,2560388359,1176283,SRX11050986,SRS9118954,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.94226,,0.13504,,0.80474,,0.55557,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64495,SRR14713039,SRX11050985,SRS9118953,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 heterozygous [het4],GSM5353446,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,runx1 heterozygous [het4],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,GSM5353446,GSM5353446: runx1 heterozygous [het4]; Danio rerio; RNA Seq,GSM5353446,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353446,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=het4 S7 L001 I1 001.fastq.gz   read2PairFiles=het4 S7 L001 R1 001.fastq.gz   read3PairFiles=het4 S7 L001 R2 001.fastq.gz,het4_S7_L001_I1_001.fastq.gz het4_S7_L001_R1_001.fastq.gz het4_S7_L001_R2_001.fastq.gz,fastq fastq fastq,14439557666.0,114492061.0,GSM5353446 r1,0:8 1:27.58 2:90.53,A:2881879087;C:2363134128;G:2454028728;T:2665247080;N:1231872,8,27,90,,2881879087,2363134128,2454028728,2665247080,1231872,SRX11050985,SRS9118953,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.94724,,0.10407,,0.81933,,0.54039,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64496,SRR14713040,SRX11050985,SRS9118953,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 heterozygous [het4],GSM5353446,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,runx1 heterozygous [het4],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,GSM5353446,GSM5353446: runx1 heterozygous [het4]; Danio rerio; RNA Seq,GSM5353446,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353446,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=het4 S7 L002 I1 001.fastq.gz   read2PairFiles=het4 S7 L002 R1 001.fastq.gz   read3PairFiles=het4 S7 L002 R2 001.fastq.gz,het4_S7_L002_I1_001.fastq.gz het4_S7_L002_R1_001.fastq.gz het4_S7_L002_R2_001.fastq.gz,fastq fastq fastq,14516825269.0,115104734.0,GSM5353446 r2,0:8 1:27.58 2:90.53,A:2897098851;C:2375923349;G:2467885484;T:2678832367;N:1255959,8,27,90,,2897098851,2375923349,2467885484,2678832367,1255959,SRX11050985,SRS9118953,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.94771,,0.1046,,0.81815,,0.54278,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64497,SRR14713037,SRX11050984,SRS9118952,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 heterozygous [het3],GSM5353445,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,runx1 heterozygous [het3],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,GSM5353445,GSM5353445: runx1 heterozygous [het3]; Danio rerio; RNA Seq,GSM5353445,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353445,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=het3 S5 L001 I1 001.fastq.gz   read2PairFiles=het3 S5 L001 R1 001.fastq.gz   read3PairFiles=het3 S5 L001 R2 001.fastq.gz,het3_S5_L001_I1_001.fastq.gz het3_S5_L001_R1_001.fastq.gz het3_S5_L001_R2_001.fastq.gz,fastq fastq fastq,17042594115.0,135113383.0,GSM5353445 r1,0:8 1:27.58 2:90.55,A:3495680489;C:2705535785;G:2814514030;T:3217929561;N:1467829,8,27,90,,3495680489,2705535785,2814514030,3217929561,1467829,SRX11050984,SRS9118952,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.9429,,0.13005,,0.80521,,0.58007,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
64498,SRR14713038,SRX11050984,SRS9118952,SRP322388,PRJNA734619,Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [II],GSE176036,Transcriptome Analysis,Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC  but how such clones expand is unclear. Here  we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes  like asxl1  promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator  nr4a1  abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of germline runx1 homozygous mutant hematopoiesis compared to runx1 heterozygous hematopoiesis. Embryos from runx1 heterozygous incross were grown to maturity. Whole kidney marrow cells from 4 runx1 heterozygous and 4 runx1 homozygous mutant zebrafish were collected for preparation for 10x single cell RNA sequencing.,parent bioproject:PRJNA734615,pubmed:34735227,,runx1 heterozygous [het3],GSM5353445,,tissue:unsorted whole kidney marrow cells|cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,runx1 heterozygous [het3],The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0. Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets  gene level count values were summed to retain a final count matrix of 21 727 features across 35 178 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 250 genes per cell; 3 >= 0.75 novelty score  calculated as log10genes detected / log10UMI counts per cell; and 4 <= 15 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: Count matrices from the NovaSeq platform.,unsorted whole kidney marrow cells,No additional treatment for unsorted cells.,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month.,cell type:unsorted whole kidney marrow cells|sorting:unsorted|age:8 month|genotype:runx1 heterozygous,GSM5353445,GSM5353445: runx1 heterozygous [het3]; Danio rerio; RNA Seq,GSM5353445,,1,post euthanasia  the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin  placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellets were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products  then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 6 000 cells per reaction. We followed the 10x Genomics sample preparation protocol and the 10x Genomics single cell RNA sequencing v3.1 library preparation.,GEO Accession:GSM5353445,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP322388,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=het3 S5 L002 I1 001.fastq.gz   read2PairFiles=het3 S5 L002 R1 001.fastq.gz   read3PairFiles=het3 S5 L002 R2 001.fastq.gz,het3_S5_L002_I1_001.fastq.gz het3_S5_L002_R1_001.fastq.gz het3_S5_L002_R2_001.fastq.gz,fastq fastq fastq,17107136510.0,135624932.0,GSM5353445 r2,0:8 1:27.58 2:90.55,A:3508835537;C:2715993447;G:2825882388;T:3229265829;N:1498996,8,27,90,,3508835537,2715993447,2825882388,3229265829,1498996,SRX11050984,SRS9118952,SRA1239845,GEO,"Oncology/Hematology, Boston Children's Hospital",1,0.94177,,0.13016,,0.80393,,0.57731,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-06-02,Adult,Adult,Kidney,Renal System
65966,SRR15712664,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-1_S1_L004_R1_001.fastq.gz six2_rds-1_S1_L004_R2_001.fastq.gz,fastq fastq,19349955000.0,64499850.0,GSM5556587 r1,0:150 1:150,A:7162489449;C:3375746042;G:3279440705;T:5531862071;N:416733,150,150,,,7162489449,3375746042,3279440705,5531862071,416733,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87809,0.0,0.21463,1.0,0.79689,,0.57444,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65967,SRR15712665,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-8_S1_L003_R1_001.fastq.gz six2_rds-8_S1_L003_R2_001.fastq.gz,fastq fastq,7105754400.0,23685848.0,GSM5556587 r10,0:150 1:150,A:2387232028;C:1255873597;G:1185129014;T:2277402001;N:117760,150,150,,,2387232028,1255873597,1185129014,2277402001,117760,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87582,0.0,0.20979,1.0,0.79782,,0.57685,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65968,SRR15712666,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-10_S1_L004_R1_001.fastq.gz six2_rds-10_S1_L004_R2_001.fastq.gz,fastq fastq,16440541800.0,54801806.0,GSM5556587 r11,0:150 1:150,A:6463236336;C:2798496412;G:2707975748;T:4470288383;N:544921,150,150,,,6463236336,2798496412,2707975748,4470288383,544921,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87902,0.0,0.21509,1.0,0.79395,,0.56582,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65969,SRR15712667,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-12_S1_L004_R1_001.fastq.gz six2_rds-12_S1_L004_R2_001.fastq.gz,fastq fastq,13212121800.0,44040406.0,GSM5556587 r12,0:150 1:150,A:5196898881;C:2253733071;G:2178536712;T:3582512811;N:440325,150,150,,,5196898881,2253733071,2178536712,3582512811,440325,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87751,0.0,0.21742,1.0,0.79555,,0.57537,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65970,SRR15712668,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-5_S1_L003_R1_001.fastq.gz six2_rds-5_S1_L003_R2_001.fastq.gz,fastq fastq,4853709900.0,16179033.0,GSM5556587 r2,0:150 1:150,A:1629549441;C:854657489;G:808913312;T:1560509625;N:80033,150,150,,,1629549441,854657489,808913312,1560509625,80033,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87494,0.0,0.2093,1.0,0.79732,,0.57664,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65971,SRR15712669,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-6_S1_L003_R1_001.fastq.gz six2_rds-6_S1_L003_R2_001.fastq.gz,fastq fastq,4426652700.0,14755509.0,GSM5556587 r3,0:150 1:150,A:1488160218;C:776137895;G:733825816;T:1428454088;N:74683,150,150,,,1488160218,776137895,733825816,1428454088,74683,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87652,0.0,0.21116,1.0,0.79683,,0.56354,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65972,SRR15712670,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-7_S1_L003_R1_001.fastq.gz six2_rds-7_S1_L003_R2_001.fastq.gz,fastq fastq,5590773600.0,18635912.0,GSM5556587 r4,0:150 1:150,A:1874947755;C:993323119;G:937833797;T:1784578957;N:89972,150,150,,,1874947755,993323119,937833797,1784578957,89972,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87537,0.0,0.20998,1.0,0.79709,,0.57129,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65973,SRR15712671,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-4_S1_L004_R1_001.fastq.gz six2_rds-4_S1_L004_R2_001.fastq.gz,fastq fastq,27727785600.0,92425952.0,GSM5556587 r5,0:150 1:150,A:10270684071;C:4847064738;G:4699231120;T:7910210723;N:594948,150,150,,,10270684071,4847064738,4699231120,7910210723,594948,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87788,0.0,0.2132,1.0,0.7964,,0.5547,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65974,SRR15712672,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-9_S1_L004_R1_001.fastq.gz six2_rds-9_S1_L004_R2_001.fastq.gz,fastq fastq,10680994800.0,35603316.0,GSM5556587 r6,0:150 1:150,A:4185708484;C:1812781715;G:1759282524;T:2922861803;N:360274,150,150,,,4185708484,1812781715,1759282524,2922861803,360274,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87846,0.0,0.21877,1.0,0.79462,,0.54801,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65975,SRR15712673,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-2_S1_L004_R1_001.fastq.gz six2_rds-2_S1_L004_R2_001.fastq.gz,fastq fastq,18583908600.0,61946362.0,GSM5556587 r7,0:150 1:150,A:6877604898;C:3234678896;G:3142926939;T:5328297692;N:400175,150,150,,,6877604898,3234678896,3142926939,5328297692,400175,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87774,0.0,0.2132,1.0,0.79691,,0.57302,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65976,SRR15712674,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-3_S1_L004_R1_001.fastq.gz six2_rds-3_S1_L004_R2_001.fastq.gz,fastq fastq,21811253100.0,72704177.0,GSM5556587 r8,0:150 1:150,A:8074244881;C:3827725258;G:3708040652;T:6200771782;N:470527,150,150,,,8074244881,3827725258,3708040652,6200771782,470527,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87572,0.0,0.2138,1.0,0.79989,,0.5431,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
65977,SRR15712675,SRX12008335,SRS10014485,SRP335554,PRJNA760458,adult zebrafish kidney cells,GSE183382,Other,To illustrate the functions of the various cell types in the zebrafish kidney  we sequenced the kidney cells by single cell messenger RNA sequencing. Six randomly selected zebrafish kidneys were used and obtained about 7 147 cells for RNA sequencing using a modified version of the cell expression by linear amplification and sequencing CEL seq method and incorporating unique molecular identifiers to count the transcripts. Overall design: the type of zebrafish kidney cells,,pubmed:36645741,,zebrafish kidney cells,GSM5556587,,source name:adult zebrafish kedney cells|strain:AB|tissue:kidney|developmental stage:6 month,zebrafish kidney cells,Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions Illumina The Seurat package was used to normalize data  dimensionality reduction  clustering  differential expression. Genome build: danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene,adult zebrafish kedney cells,,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer’s instructions 10× Chromium Controller 10X Genomics,Zebrafish were maintained in standard conditions under a 14 hours light and 10 hours dark cycle and fed three times daily,strain:AB|tissue:kidney|developmental stage:6 month,GSM5556587,GSM5556587: zebrafish kidney cells; Danio rerio; RNA Seq,GSM5556587,,1,Kidney cells from 6 randomly selected zebrafish was loaded into Chromium microfluidic chips with 30 v chemistry. sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit 10X Genomics according to the manufacturer's instructions 10× Chromium Controller 10X Genomics,GEO Accession:GSM5556587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP335554,,,six2_rds-11_S1_L004_R1_001.fastq.gz six2_rds-11_S1_L004_R2_001.fastq.gz,fastq fastq,11680783800.0,38935946.0,GSM5556587 r9,0:150 1:150,A:4586348762;C:1986953331;G:1925942390;T:3181153183;N:386134,150,150,,,4586348762,1986953331,1925942390,3181153183,386134,SRX12008335,SRS10014485,SRA1288506,GEO,"Xinqiao Hospital, Army Medical University (Third Military Medical University)",2,0.0,0.87701,0.0,0.21502,1.0,0.79703,,0.57704,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-09-03,Adult,Adult,Kidney,Renal System
67709,SRR17247457,SRX13426490,SRS11327478,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish nov2019 mcs 2,GSM5737714,,source name:zebrafish kidney marrow|Stage:adult|class:mcs/control|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish nov2019 mcs 2,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:mcs/control|tissue:kidney marrow,GSM5737714,GSM5737714: zfish nov2019 mcs 2; Danio rerio; RNA Seq,GSM5737714 r1,GSM5737714,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,m_2_S4_L001_R1_001.fastq.gz m_2_S4_L001_R2_001.fastq.gz,fastq fastq,30896010944.0,102304672.0,GSM5737714 r1,0:151 1:151,A:7831986052;C:6707621804;G:6407553174;T:9948342840;N:507074,151,151,,,7831986052,6707621804,6407553174,9948342840,507074,SRX13426490,SRS11327478,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.0362,0.95501,0.00505,0.13634,0.9978,0.87235,0.71964,0.7275,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67710,SRR17247458,SRX13426490,SRS11327478,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish nov2019 mcs 2,GSM5737714,,source name:zebrafish kidney marrow|Stage:adult|class:mcs/control|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish nov2019 mcs 2,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:mcs/control|tissue:kidney marrow,GSM5737714,GSM5737714: zfish nov2019 mcs 2; Danio rerio; RNA Seq,GSM5737714 r1,GSM5737714,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,m_2_S4_L002_R1_001.fastq.gz m_2_S4_L002_R2_001.fastq.gz,fastq fastq,31427224716.0,104063658.0,GSM5737714 r2,0:151 1:151,A:7951620974;C:6826123654;G:6471292663;T:10177703459;N:483966,151,151,,,7951620974,6826123654,6471292663,10177703459,483966,SRX13426490,SRS11327478,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.03694,0.95444,0.00516,0.13567,0.99734,0.87326,0.75563,0.74575,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67711,SRR17247459,SRX13426489,SRS11327476,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish nov2019 mcs 1,GSM5737713,,source name:zebrafish kidney marrow|Stage:adult|class:mcs/control|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish nov2019 mcs 1,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:mcs/control|tissue:kidney marrow,GSM5737713,GSM5737713: zfish nov2019 mcs 1; Danio rerio; RNA Seq,GSM5737713 r1,GSM5737713,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,m_1_S3_L001_R1_001.fastq.gz m_1_S3_L001_R2_001.fastq.gz,fastq fastq,33350512622.0,110432161.0,GSM5737713 r1,0:151 1:151,A:8360198472;C:7386110257;G:7035347185;T:10568307654;N:549054,151,151,,,8360198472,7386110257,7035347185,10568307654,549054,SRX13426489,SRS11327476,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.03922,0.9568,0.00551,0.13993,0.99746,0.87986,0.74609,0.82701,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67712,SRR17247460,SRX13426489,SRS11327476,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish nov2019 mcs 1,GSM5737713,,source name:zebrafish kidney marrow|Stage:adult|class:mcs/control|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish nov2019 mcs 1,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:mcs/control|tissue:kidney marrow,GSM5737713,GSM5737713: zfish nov2019 mcs 1; Danio rerio; RNA Seq,GSM5737713 r1,GSM5737713,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,m_1_S3_L002_R1_001.fastq.gz m_1_S3_L002_R2_001.fastq.gz,fastq fastq,33891533844.0,112223622.0,GSM5737713 r2,0:151 1:151,A:8478231309;C:7511148473;G:7106223638;T:10795407036;N:523388,151,151,,,8478231309,7511148473,7106223638,10795407036,523388,SRX13426489,SRS11327476,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.04314,0.95776,0.00612,0.13878,0.99748,0.88034,0.73313,0.82614,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67713,SRR17247461,SRX13426488,SRS11327475,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish nov2019 cxcl8 2,GSM5737712,,source name:zebrafish kidney marrow|Stage:adult|class:cxcl8|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish nov2019 cxcl8 2,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:cxcl8|tissue:kidney marrow,GSM5737712,GSM5737712: zfish nov2019 cxcl8 2; Danio rerio; RNA Seq,GSM5737712 r1,GSM5737712,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,8_2_S2_L001_R1_001.fastq.gz 8_2_S2_L001_R2_001.fastq.gz,fastq fastq,33608129796.0,111285198.0,GSM5737712 r1,0:151 1:151,A:8722877609;C:6922385996;G:6668063034;T:11294249015;N:554142,151,151,,,8722877609,6922385996,6668063034,11294249015,554142,SRX13426488,SRS11327475,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02552,0.94052,0.0043,0.14674,0.9976,0.86466,0.72964,0.733,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67714,SRR17247462,SRX13426488,SRS11327475,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish nov2019 cxcl8 2,GSM5737712,,source name:zebrafish kidney marrow|Stage:adult|class:cxcl8|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish nov2019 cxcl8 2,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:cxcl8|tissue:kidney marrow,GSM5737712,GSM5737712: zfish nov2019 cxcl8 2; Danio rerio; RNA Seq,GSM5737712 r1,GSM5737712,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,8_2_S2_L002_R1_001.fastq.gz 8_2_S2_L002_R2_001.fastq.gz,fastq fastq,34101912178.0,112920239.0,GSM5737712 r2,0:151 1:151,A:8834924454;C:7026706140;G:6723081178;T:11516672500;N:527906,151,151,,,8834924454,7026706140,6723081178,11516672500,527906,SRX13426488,SRS11327475,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02981,0.94163,0.00539,0.14603,0.99744,0.86545,0.72068,0.74612,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67715,SRR17247463,SRX13426487,SRS11327474,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish nov2019 cxcl8 1,GSM5737711,,source name:zebrafish kidney marrow|Stage:adult|class:cxcl8|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish nov2019 cxcl8 1,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:cxcl8|tissue:kidney marrow,GSM5737711,GSM5737711: zfish nov2019 cxcl8 1; Danio rerio; RNA Seq,GSM5737711 r1,GSM5737711,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,8_1_S1_L001_R1_001.fastq.gz 8_1_S1_L001_R2_001.fastq.gz,fastq fastq,36951871984.0,122357192.0,GSM5737711 r1,0:151 1:151,A:9626031126;C:7570369217;G:7302558662;T:12452305774;N:607205,151,151,,,9626031126,7570369217,7302558662,12452305774,607205,SRX13426487,SRS11327474,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02737,0.93641,0.00404,0.1541,0.99736,0.85508,0.7563,0.72637,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67716,SRR17247464,SRX13426487,SRS11327474,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish nov2019 cxcl8 1,GSM5737711,,source name:zebrafish kidney marrow|Stage:adult|class:cxcl8|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish nov2019 cxcl8 1,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:cxcl8|tissue:kidney marrow,GSM5737711,GSM5737711: zfish nov2019 cxcl8 1; Danio rerio; RNA Seq,GSM5737711 r1,GSM5737711,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,8_1_S1_L002_R1_001.fastq.gz 8_1_S1_L002_R2_001.fastq.gz,fastq fastq,37469129128.0,124069964.0,GSM5737711 r2,0:151 1:151,A:9743940391;C:7679263985;G:7358502754;T:12686838441;N:583557,151,151,,,9743940391,7679263985,7358502754,12686838441,583557,SRX13426487,SRS11327474,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02963,0.93729,0.00529,0.15304,0.99734,0.85492,0.71942,0.71806,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67717,SRR17247465,SRX13426486,SRS11327472,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish km july2020 prkcda 2 gex,GSM5737710,,source name:zebrafish kidney marrow|Stage:adult|class:prkcda|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish km july2020 prkcda 2 gex,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:prkcda|tissue:kidney marrow,GSM5737710,GSM5737710: zfish km july2020 prkcda 2 gex; Danio rerio; RNA Seq,GSM5737710 r1,GSM5737710,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,prkcda_2_gex_S2_L001_R1_001.fastq.gz prkcda_2_gex_S2_L001_R2_001.fastq.gz,fastq fastq,13835729850.0,45813675.0,GSM5737710 r1,0:151 1:151,A:3702098746;C:2530292707;G:2281467337;T:5321602811;N:268249,151,151,,,3702098746,2530292707,2281467337,5321602811,268249,SRX13426486,SRS11327472,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02335,0.84758,0.00679,0.11459,0.99159,0.81793,0.56734,0.57225,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67718,SRR17247466,SRX13426486,SRS11327472,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish km july2020 prkcda 2 gex,GSM5737710,,source name:zebrafish kidney marrow|Stage:adult|class:prkcda|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish km july2020 prkcda 2 gex,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:prkcda|tissue:kidney marrow,GSM5737710,GSM5737710: zfish km july2020 prkcda 2 gex; Danio rerio; RNA Seq,GSM5737710 r1,GSM5737710,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,prkcda_2_gex_S2_L002_R1_001.fastq.gz prkcda_2_gex_S2_L002_R2_001.fastq.gz,fastq fastq,12732723472.0,42161336.0,GSM5737710 r2,0:151 1:151,A:3401432115;C:2329599383;G:2131111574;T:4870319578;N:260822,151,151,,,3401432115,2329599383,2131111574,4870319578,260822,SRX13426486,SRS11327472,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.01889,0.8502,0.00458,0.11409,0.99239,0.81708,0.56652,0.5669,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67719,SRR17247467,SRX13426485,SRS11327473,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish km july2020 prkcda 1 gex,GSM5737709,,source name:zebrafish kidney marrow|Stage:adult|class:prkcda|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish km july2020 prkcda 1 gex,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:prkcda|tissue:kidney marrow,GSM5737709,GSM5737709: zfish km july2020 prkcda 1 gex; Danio rerio; RNA Seq,GSM5737709 r1,GSM5737709,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,prkcda_1_gex_S1_L001_R1_001.fastq.gz prkcda_1_gex_S1_L001_R2_001.fastq.gz,fastq fastq,14142779894.0,46830397.0,GSM5737709 r1,0:151 1:151,A:3803907364;C:2547631786;G:2315347877;T:5475620885;N:271982,151,151,,,3803907364,2547631786,2315347877,5475620885,271982,SRX13426485,SRS11327473,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02414,0.84338,0.00622,0.11548,0.99097,0.8144,0.62514,0.57188,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67720,SRR17247468,SRX13426485,SRS11327473,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish km july2020 prkcda 1 gex,GSM5737709,,source name:zebrafish kidney marrow|Stage:adult|class:prkcda|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish km july2020 prkcda 1 gex,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:prkcda|tissue:kidney marrow,GSM5737709,GSM5737709: zfish km july2020 prkcda 1 gex; Danio rerio; RNA Seq,GSM5737709 r1,GSM5737709,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,prkcda_1_gex_S1_L002_R1_001.fastq.gz prkcda_1_gex_S1_L002_R2_001.fastq.gz,fastq fastq,13035917882.0,43165291.0,GSM5737709 r2,0:151 1:151,A:3500572922;C:2349111864;G:2165763483;T:5020201575;N:268038,151,151,,,3500572922,2349111864,2165763483,5020201575,268038,SRX13426485,SRS11327473,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02024,0.84227,0.00588,0.1153,0.99289,0.81746,0.60227,0.56302,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67721,SRR17247469,SRX13426484,SRS11327471,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish km july2020 mcs 2 gex,GSM5737708,,source name:zebrafish kidney marrow|Stage:adult|class:mcs/control|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish km july2020 mcs 2 gex,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:mcs/control|tissue:kidney marrow,GSM5737708,GSM5737708: zfish km july2020 mcs 2 gex; Danio rerio; RNA Seq,GSM5737708 r1,GSM5737708,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,mcs_2_gex_S4_L001_R1_001.fastq.gz mcs_2_gex_S4_L001_R2_001.fastq.gz,fastq fastq,16896987882.0,55950291.0,GSM5737708 r1,0:151 1:151,A:4591971940;C:3075167390;G:2821138917;T:6408383413;N:326222,151,151,,,4591971940,3075167390,2821138917,6408383413,326222,SRX13426484,SRS11327471,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02543,0.89539,0.00682,0.1299,0.99019,0.79162,0.58431,0.57222,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67722,SRR17247470,SRX13426484,SRS11327471,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish km july2020 mcs 2 gex,GSM5737708,,source name:zebrafish kidney marrow|Stage:adult|class:mcs/control|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish km july2020 mcs 2 gex,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:mcs/control|tissue:kidney marrow,GSM5737708,GSM5737708: zfish km july2020 mcs 2 gex; Danio rerio; RNA Seq,GSM5737708 r1,GSM5737708,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,mcs_2_gex_S4_L002_R1_001.fastq.gz mcs_2_gex_S4_L002_R2_001.fastq.gz,fastq fastq,15528315124.0,51418262.0,GSM5737708 r2,0:151 1:151,A:4211257903;C:2827053832;G:2631217951;T:5858464915;N:320523,151,151,,,4211257903,2827053832,2631217951,5858464915,320523,SRX13426484,SRS11327471,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02206,0.89665,0.00561,0.13079,0.99149,0.79178,0.59462,0.56762,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67723,SRR17247471,SRX13426483,SRS11327470,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish km july2020 mcs 1 gex,GSM5737707,,source name:zebrafish kidney marrow|Stage:adult|class:mcs/control|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish km july2020 mcs 1 gex,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:mcs/control|tissue:kidney marrow,GSM5737707,GSM5737707: zfish km july2020 mcs 1 gex; Danio rerio; RNA Seq,GSM5737707 r1,GSM5737707,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,mcs_1_gex_S3_L001_R1_001.fastq.gz mcs_1_gex_S3_L001_R2_001.fastq.gz,fastq fastq,20942692528.0,69346664.0,GSM5737707 r1,0:151 1:151,A:5740347455;C:3760947039;G:3428436604;T:8012559458;N:401972,151,151,,,5740347455,3760947039,3428436604,8012559458,401972,SRX13426483,SRS11327470,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02601,0.88017,0.00646,0.1351,0.98959,0.79711,0.62833,0.56309,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Adult,Adult,Kidney,Renal System
67724,SRR17247472,SRX13426483,SRS11327470,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,zfish km july2020 mcs 1 gex,GSM5737707,,source name:zebrafish kidney marrow|Stage:adult|class:mcs/control|tissue:kidney marrow|geo loc name:missing|collection date:missing,zfish km july2020 mcs 1 gex,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,zebrafish kidney marrow,No treatments,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Fish were maintained on a recirculating water system at 28C.,Stage:adult|class:mcs/control|tissue:kidney marrow,GSM5737707,GSM5737707: zfish km july2020 mcs 1 gex; Danio rerio; RNA Seq,GSM5737707 r1,GSM5737707,1,Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,mcs_1_gex_S3_L002_R1_001.fastq.gz mcs_1_gex_S3_L002_R2_001.fastq.gz,fastq fastq,19312854398.0,63949849.0,GSM5737707 r2,0:151 1:151,A:5284897528;C:3469277015;G:3207797556;T:7350475426;N:406873,151,151,,,5284897528,3469277015,3207797556,7350475426,406873,SRX13426483,SRS11327470,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.02195,0.88364,0.00566,0.1347,0.99127,0.79799,0.63511,0.57074,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,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 Huët 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 Huët 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.,,pubmed:40020188,,km  cmyb pu.1  replicate 1,GSM6267523,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.54286,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  cmyb pu.1  replicate 1,GSM6267523,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.53444,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  cmyb pu.1  replicate 1,GSM6267523,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.53674,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  cmyb pu.1  replicate 1,GSM6267523,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.52704,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  pu.1  replicate 1,GSM6267522,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.51501,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  pu.1  replicate 1,GSM6267522,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.50946,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  pu.1  replicate 1,GSM6267522,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.51636,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  pu.1  replicate 1,GSM6267522,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.52682,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  cmyb  replicate 1,GSM6267521,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.5179,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  cmyb  replicate 1,GSM6267521,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.52084,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  cmyb  replicate 1,GSM6267521,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.51904,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  cmyb  replicate 1,GSM6267521,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.51722,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  wildtype  replicate 1,GSM6267520,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.46343,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  wildtype  replicate 1,GSM6267520,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.47032,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  wildtype  replicate 1,GSM6267520,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.47011,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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 Huët 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 Huët 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.,,pubmed:40020188,,km  wildtype  replicate 1,GSM6267520,,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’s 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 ≥40000 or mitochondrial gene percent ≥15% 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 “LogNormalize” 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,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ 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® 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.,,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 μm cell strainer. The cells were counted and the proportion of living cells was calculated. post ensuring that the proportion of living cells was ≥90%  the cell concentration was adjusted to 1 000 cells/μL. 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® 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP383719,,,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,,,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,,0.46543,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-06-27,Adult,Adult,Kidney,Renal System
72561,SRR22722190,SRX18683720,SRS16126888,SRP412911,PRJNA911847,Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia,PRJNA911847,Other,Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic  functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity  full blown leukemia ensued with multi lineage dysplasia  increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing  differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion  the zebrafish models of IDH2 mutated AML recapitulated the morphologic  clinical  functional and transcriptomic characteristics of human diseases  and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening,,,,,Transgenic FLT3 ITD IDH2 R140Q,,strain:TU|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 month|dev stage:8 month|sex:pooled male and female|tissue:kidney marrow|genotype:Transgenic Runx1:FLT3ITDIDH2R140Q|BioSampleModel:Model organism or animal,,,,,,,,,Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R140Q,ITD140Q,ITD140Q,Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics  Pleasanton  CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers  followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI  HK  China.,,,OTHER,TRANSCRIPTOMIC,other,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP412911,,loader:fastq load.py,ITD172KA_S1_L001_I1_001.fastq.gz ITD172KA_S1_L001_R1_001.fastq.gz ITD172KA_S1_L001_R2_001.fastq.gz,fastq fastq fastq,52149830422.0,410628586.0,ITD172KA S1 L001 I1 001.fastq.gz,0:8 1:28 2:91,A:10282953217;C:8459559201;G:8851285287;T:9772343870;N:1059751,8,28,91,,10282953217,8459559201,8851285287,9772343870,1059751,SRX18683720,SRS16126888,SRA1558824,The University of Hong Kong|Department of Medicine,The University of Hong Kong,1,0.88465,,0.13112,,0.81789,,0.55842,,91,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,China,2022-12-14,Adult,Adult,Kidney,Renal System
72562,SRR22722191,SRX18683719,SRS16126887,SRP412911,PRJNA911847,Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia,PRJNA911847,Other,Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic  functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity  full blown leukemia ensued with multi lineage dysplasia  increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing  differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion  the zebrafish models of IDH2 mutated AML recapitulated the morphologic  clinical  functional and transcriptomic characteristics of human diseases  and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening,,,,,Transgenic FLT3 ITD IDH2 R172K,,strain:TU|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 month|dev stage:8 month|sex:pooled male and female|tissue:kidney marrow|genotype:Transgenic Runx1:FLT3ITDIDH2R172K|BioSampleModel:Model organism or animal,,,,,,,,,Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R172K,ITD172K,ITD172K,Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics  Pleasanton  CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers  followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI  HK  China.,,,OTHER,TRANSCRIPTOMIC,other,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP412911,,loader:fastq load.py,ITD140QA_S1_L004_I1_001.fastq.gz ITD140QA_S1_L004_R1_001.fastq.gz ITD140QA_S1_L004_R2_001.fastq.gz,fastq fastq fastq,28595025233.0,225157679.0,ITD140QA S1 L004 I1 001.fastq.gz,0:8 1:28 2:91,A:5628987577;C:4565848641;G:4959209904;T:5302394659;N:32908008,8,28,91,,5628987577,4565848641,4959209904,5302394659,32908008,SRX18683719,SRS16126887,SRA1558824,The University of Hong Kong|Department of Medicine,The University of Hong Kong,1,0.81404,,0.11315,,0.83327,,0.56222,,91,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,China,2022-12-13,Adult,Adult,Kidney,Renal System
72563,SRR22722192,SRX18683718,SRS16126886,SRP412911,PRJNA911847,Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia,PRJNA911847,Other,Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic  functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity  full blown leukemia ensued with multi lineage dysplasia  increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing  differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion  the zebrafish models of IDH2 mutated AML recapitulated the morphologic  clinical  functional and transcriptomic characteristics of human diseases  and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening,,,,,Wild type,,strain:TU|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 month|dev stage:8 month|sex:pooled male and female|tissue:kidney marrow|genotype:Wild type|BioSampleModel:Model organism or animal,,,,,,,,,Single cell RNA seq of Danio rerio: Wild type,Control,Control,Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics  Pleasanton  CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers  followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI  HK  China.,,,OTHER,TRANSCRIPTOMIC,other,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP412911,,loader:fastq load.py,ControlA_S1_L003_R2_001.fastq.gz ControlA_S1_L003_R1_001.fastq.gz ControlA_S1_L003_I1_001.fastq.gz,fastq fastq fastq,37892727491.0,298367933.0,ControlA S1 L003 I1 001.fastq.gz,0:8 1:28 2:91,A:7386602298;C:6174680460;G:6579652828;T:6955791213;N:54755104,8,28,91,,7386602298,6174680460,6579652828,6955791213,54755104,SRX18683718,SRS16126886,SRA1558824,The University of Hong Kong|Department of Medicine,The University of Hong Kong,1,0.81686,,0.11049,,0.84139,,0.46084,,91,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,China,2022-12-14,Adult,Adult,Kidney,Renal System