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49 rows where experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Marrow"

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technology 3

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devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Marrow · 49 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 49 ✖

experiment.library_selection 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
59301 59301 SRR11851897 SRX8402007 SRS6714764 SRP264841 PRJNA635161 Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq] GSE151231 Transcriptome Analysis Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells. parent bioproject:PRJNA635158 pubmed:34170284   scRNA seq gata2b ko 3 GSM4568915   tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko scRNA seq gata2b ko 3 The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds sorted marrow cells Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing. post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops Freshly isolated kidney marrow cells from euthanized adult zebrafish. cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko GSM4568915 GSM4568915: scRNA seq gata2b ko 3; Danio rerio; RNA Seq GSM4568915   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. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops GEO Accession:GSM4568915 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP264841   loader:fastq load.py|options: appendBCtoName KO3_Single_Cell_GAGACGGA.fastq.sorted.fastq.gz fastq 3768784245.0 63353331.0 GSM4568915 r1 0:59.49 A:1049235928;C:815061845;G:790664763;T:1113812557;N:9152 59       1049235928 815061845 790664763 1113812557 9152 SRX8402007 SRS6714764 SRA1080050 GEO Oncology/Hematology, Boston Children's Hospital 1 0.9009   0.07395   0.83524   0.54215   60   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2020-05-26 Adult Adult Marrow Renal System
59302 59302 SRR11851896 SRX8402006 SRS6714763 SRP264841 PRJNA635161 Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq] GSE151231 Transcriptome Analysis Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells. parent bioproject:PRJNA635158 pubmed:34170284   scRNA seq gata2b ko 2 GSM4568914   tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko scRNA seq gata2b ko 2 The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds sorted marrow cells Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing. post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops Freshly isolated kidney marrow cells from euthanized adult zebrafish. cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko GSM4568914 GSM4568914: scRNA seq gata2b ko 2; Danio rerio; RNA Seq GSM4568914   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. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops GEO Accession:GSM4568914 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP264841   loader:fastq load.py|options: appendBCtoName KO2_Single_Cell_TTACCTCC.fastq.sorted.fastq.gz fastq 5788926123.0 96793878.0 GSM4568914 r1 0:59.81 A:1591846184;C:1284226924;G:1217400432;T:1695437315;N:15268 59       1591846184 1284226924 1217400432 1695437315 15268 SRX8402006 SRS6714763 SRA1080050 GEO Oncology/Hematology, Boston Children's Hospital 1 0.90311   0.0768   0.82227   0.56806   61   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2020-05-26 Adult Adult Marrow Renal System
59303 59303 SRR11851895 SRX8402005 SRS6714762 SRP264841 PRJNA635161 Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq] GSE151231 Transcriptome Analysis Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells. parent bioproject:PRJNA635158 pubmed:34170284   scRNA seq gata2b ko 1 GSM4568913   tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko scRNA seq gata2b ko 1 The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds sorted marrow cells Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing. post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops Freshly isolated kidney marrow cells from euthanized adult zebrafish. cell type:sorted marrow cells|age:4 mpf|genotype:gata2b ko GSM4568913 GSM4568913: scRNA seq gata2b ko 1; Danio rerio; RNA Seq GSM4568913   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. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops GEO Accession:GSM4568913 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP264841   loader:fastq load.py|options: appendBCtoName KO1_Single_Cell_TAAGGCTC.fastq.sorted.fastq.gz fastq 4485434923.0 75329131.0 GSM4568913 r1 0:59.54 A:1245571394;C:1005814804;G:944318855;T:1289711080;N:18790 59       1245571394 1005814804 944318855 1289711080 18790 SRX8402005 SRS6714762 SRA1080050 GEO Oncology/Hematology, Boston Children's Hospital 1 0.89937   0.06305   0.83879   0.54954   61   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2020-05-26 Adult Adult Marrow Renal System
59304 59304 SRR11851894 SRX8402004 SRS6714761 SRP264841 PRJNA635161 Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq] GSE151231 Transcriptome Analysis Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells. parent bioproject:PRJNA635158 pubmed:34170284   scRNA seq gata2b het 3 GSM4568912   tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het scRNA seq gata2b het 3 The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds sorted marrow cells Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing. post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops Freshly isolated kidney marrow cells from euthanized adult zebrafish. cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het GSM4568912 GSM4568912: scRNA seq gata2b het 3; Danio rerio; RNA Seq GSM4568912   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. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops GEO Accession:GSM4568912 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP264841   loader:fastq load.py|options: appendBCtoName HET3_Single_Cell_CCTTTACT.fastq.sorted.fastq.gz fastq 3696586389.0 62109708.0 GSM4568912 r1 0:59.52 A:1054965741;C:827475497;G:744430159;T:1069699165;N:15827 59       1054965741 827475497 744430159 1069699165 15827 SRX8402004 SRS6714761 SRA1080050 GEO Oncology/Hematology, Boston Children's Hospital 1 0.89246   0.06392   0.83934   0.56422   58   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2020-05-26 Adult Adult Marrow Renal System
59305 59305 SRR11851893 SRX8402003 SRS6714760 SRP264841 PRJNA635161 Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq] GSE151231 Transcriptome Analysis Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells. parent bioproject:PRJNA635158 pubmed:34170284   scRNA seq gata2b het 2 GSM4568911   tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het scRNA seq gata2b het 2 The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds sorted marrow cells Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing. post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops Freshly isolated kidney marrow cells from euthanized adult zebrafish. cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het GSM4568911 GSM4568911: scRNA seq gata2b het 2; Danio rerio; RNA Seq GSM4568911   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. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops GEO Accession:GSM4568911 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP264841   loader:fastq load.py|options: appendBCtoName HET2_Single_Cell_CAGTTATG.fastq.sorted.fastq.gz fastq 5357974983.0 89558550.0 GSM4568911 r1 0:59.83 A:1490260317;C:1191725100;G:1122517464;T:1553457613;N:14489 59       1490260317 1191725100 1122517464 1553457613 14489 SRX8402003 SRS6714760 SRA1080050 GEO Oncology/Hematology, Boston Children's Hospital 1 0.90302   0.07865   0.82603   0.57406   61   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2020-05-26 Adult Adult Marrow Renal System
59306 59306 SRR11851892 SRX8402002 SRS6714759 SRP264841 PRJNA635161 Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq] GSE151231 Transcriptome Analysis Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells. parent bioproject:PRJNA635158 pubmed:34170284   scRNA seq gata2b het 1 GSM4568910   tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het scRNA seq gata2b het 1 The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds sorted marrow cells Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing. post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops Freshly isolated kidney marrow cells from euthanized adult zebrafish. cell type:sorted marrow cells|age:4 mpf|genotype:gata2b het GSM4568910 GSM4568910: scRNA seq gata2b het 1; Danio rerio; RNA Seq GSM4568910   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. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops GEO Accession:GSM4568910 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP264841   loader:fastq load.py|options: appendBCtoName HET1_Single_Cell_ATAGCCTT.fastq.sorted.fastq.gz fastq 4701831804.0 78923769.0 GSM4568910 r1 0:59.57 A:1307674780;C:1043797904;G:1001646002;T:1348693620;N:19498 59       1307674780 1043797904 1001646002 1348693620 19498 SRX8402002 SRS6714759 SRA1080050 GEO Oncology/Hematology, Boston Children's Hospital 1 0.90603   0.07667   0.82704   0.57543   61   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2020-05-26 Adult Adult Marrow Renal System
59307 59307 SRR11851891 SRX8402001 SRS6714758 SRP264841 PRJNA635161 Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq] GSE151231 Transcriptome Analysis Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells. parent bioproject:PRJNA635158 pubmed:34170284   scRNA seq wildtype 3 GSM4568909   tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:wildtype scRNA seq wildtype 3 The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds sorted marrow cells Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing. post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops Freshly isolated kidney marrow cells from euthanized adult zebrafish. cell type:sorted marrow cells|age:4 mpf|genotype:wildtype GSM4568909 GSM4568909: scRNA seq wildtype 3; Danio rerio; RNA Seq GSM4568909   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. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops GEO Accession:GSM4568909 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP264841   loader:fastq load.py|options: appendBCtoName WT3_Single_Cell_AGAAAGCT.fastq.sorted.fastq.gz fastq 3348785686.0 56255768.0 GSM4568909 r1 0:59.53 A:955572407;C:728586737;G:678902164;T:985710022;N:14356 59       955572407 728586737 678902164 985710022 14356 SRX8402001 SRS6714758 SRA1080050 GEO Oncology/Hematology, Boston Children's Hospital 1 0.88271   0.06967   0.8284   0.54728   61   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2020-05-26 Adult Adult Marrow Renal System
59308 59308 SRR11851890 SRX8402000 SRS6714757 SRP264841 PRJNA635161 Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq] GSE151231 Transcriptome Analysis Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells. parent bioproject:PRJNA635158 pubmed:34170284   scRNA seq wildtype 2 GSM4568908   tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:wildtype scRNA seq wildtype 2 The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds sorted marrow cells Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing. post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops Freshly isolated kidney marrow cells from euthanized adult zebrafish. cell type:sorted marrow cells|age:4 mpf|genotype:wildtype GSM4568908 GSM4568908: scRNA seq wildtype 2; Danio rerio; RNA Seq GSM4568908   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. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops GEO Accession:GSM4568908 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP264841   loader:fastq load.py|options: appendBCtoName WT2_Single_Cell_TCGCATAA.fastq.sorted.fastq.gz fastq 3812899254.0 63738225.0 GSM4568908 r1 0:59.82 A:1040969741;C:863166087;G:810647668;T:1098105772;N:9986 59       1040969741 863166087 810647668 1098105772 9986 SRX8402000 SRS6714757 SRA1080050 GEO Oncology/Hematology, Boston Children's Hospital 1 0.91023   0.06938   0.83238   0.54799   59   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2020-05-26 Adult Adult Marrow Renal System
59309 59309 SRR11851889 SRX8401999 SRS6714756 SRP264841 PRJNA635161 Gata2 loss alters epigenetic priming and gene expression profiles in early myeloid and lymphoid progenitors leading to cytopenias [RNA seq] GSE151231 Transcriptome Analysis Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias atypical infections and increased risk of hematologic malignancies. Due to embryonic lethality of Gata2 / mice the role of germline loss of GATA2 has not been studied in adult hematopoiesis. Here we generated a zebrafish mutant of gata2b which in maturity recapitulated the myelomonocytopenia and B cell lymphopenia of GATA2 syndrome. Using single cell epigenetic and transcriptomic analyses we showed that loss of gata2b alters chromosome accessibility and results in gene expression changes in both early myeloid and lymphoid progenitors. We found differentiation block with skewing away from the monocytic program in myeloid progenitors in gata2bko zebrafish. In lymphoid progenitors gata2b loss led to increased lymphoid priming but with incomplete B cell lymphopoiesis. These results place GATA2 in critical junctions of lineage specification in adult hematopoiesis. Overall design: Single cell RNA sequencing were performed on sorted zebrafish kidney marrow cell from wildtype gata2b heterozygous and gata2b homozygous mutants exon 2 CRISPR mutants described in this paper n=3 each genotype. The zebrafish underwent cardiac bleeding to reduce amount of peripheral blood in the marrow samples. Cells were sorted on BDAria2 sorter into 1x PBS with 0.04% BSA. The goal of sorting was to enrich for no mature myeloid and erythroid cell types comprising <50% of the adult marrow cells. parent bioproject:PRJNA635158 pubmed:34170284   scRNA seq wildtype 1 GSM4568907   tissue:sorted marrow cells|cell type:sorted marrow cells|age:4 mpf|genotype:wildtype scRNA seq wildtype 1 The paired end fastq files have been reorganized into a single end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode. samples were processed by the Harvard Medical School Single Cell core https://singlecellcore.hms.harvard.edu/ using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system with 75 cycle kit with pair end reads Read1: 61 cycles Read2: 14 cycles Index 1: 8 cycles Index 2: 8 cycles. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Stuart et al. 2019. Genome build: GRCz10 Supplementary files format and content: rds sorted marrow cells Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single cell core at Harvard Medical school on ice every 45 60 min for processing. post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops Freshly isolated kidney marrow cells from euthanized adult zebrafish. cell type:sorted marrow cells|age:4 mpf|genotype:wildtype GSM4568907 GSM4568907: scRNA seq wildtype 1; Danio rerio; RNA Seq GSM4568907   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. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C both sample tube being sorted and collection tube. Samples were dissected and sorted in a staggered fashion every 45 60min were kept on ice post sorting and walked to the processing core every 45 60min for processing for inDrops single cell RNA sequencing. Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single cell core. https://github.com/indrops/indrops GEO Accession:GSM4568907 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP264841   loader:fastq load.py|options: appendBCtoName WT1_Single_Cell_CTTAATAG.fastq.sorted.fastq.gz fastq 3675748091.0 61731984.0 GSM4568907 r1 0:59.54 A:1040800033;C:822608649;G:765542043;T:1046781383;N:15983 59       1040800033 822608649 765542043 1046781383 15983 SRX8401999 SRS6714756 SRA1080050 GEO Oncology/Hematology, Boston Children's Hospital 1 0.8978   0.05341   0.84167   0.59389   61   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2020-05-26 Adult Adult Marrow Renal System
69438 69438 SRR18687231 SRX14788266 SRS12547158 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       Mutant 5mpf scRNAseq GSM6035264   source name:wkm|tissue:marrow|age:5mpf|genotype:gata2a / Mutant 5mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:5mpf|genotype:gata2a / GSM6035264 GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq GSM6035264 r1 GSM6035264 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py MUTANT_S2_L001_I1_001.fastq.gz MUTANT_S2_L001_R1_001.fastq.gz MUTANT_S2_L001_R2_001.fastq.gz fastq fastq fastq 7173831982.0 56486866.0 GSM6035264 r1 0:8 1:28 2:91 A:1358934535;C:1244254049;G:1282298109;T:1250397550;N:4420563 8 28 91   1358934535 1244254049 1282298109 1250397550 4420563 SRX14788266 SRS12547158 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.96273   0.07511   0.84861   0.53711   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69439 69439 SRR18687232 SRX14788266 SRS12547158 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       Mutant 5mpf scRNAseq GSM6035264   source name:wkm|tissue:marrow|age:5mpf|genotype:gata2a / Mutant 5mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:5mpf|genotype:gata2a / GSM6035264 GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq GSM6035264 r1 GSM6035264 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py MUTANT_S2_L002_I1_001.fastq.gz MUTANT_S2_L002_R1_001.fastq.gz MUTANT_S2_L002_R2_001.fastq.gz fastq fastq fastq 7052205352.0 55529176.0 GSM6035264 r2 0:8 1:28 2:91 A:1335427840;C:1223120616;G:1262490348;T:1228023814;N:4092398 8 28 91   1335427840 1223120616 1262490348 1228023814 4092398 SRX14788266 SRS12547158 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.96332   0.07559   0.84869   0.53571   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69440 69440 SRR18687233 SRX14788266 SRS12547158 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       Mutant 5mpf scRNAseq GSM6035264   source name:wkm|tissue:marrow|age:5mpf|genotype:gata2a / Mutant 5mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:5mpf|genotype:gata2a / GSM6035264 GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq GSM6035264 r1 GSM6035264 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py MUTANT_S2_L003_I1_001.fastq.gz MUTANT_S2_L003_R1_001.fastq.gz MUTANT_S2_L003_R2_001.fastq.gz fastq fastq fastq 7121271889.0 56073007.0 GSM6035264 r3 0:8 1:28 2:91 A:1348956241;C:1235761797;G:1273552429;T:1240317702;N:4055468 8 28 91   1348956241 1235761797 1273552429 1240317702 4055468 SRX14788266 SRS12547158 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.96323   0.07544   0.84776   0.54532   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69441 69441 SRR18687234 SRX14788266 SRS12547158 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       Mutant 5mpf scRNAseq GSM6035264   source name:wkm|tissue:marrow|age:5mpf|genotype:gata2a / Mutant 5mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:5mpf|genotype:gata2a / GSM6035264 GSM6035264: Mutant 5mpf scRNAseq; Danio rerio; RNA Seq GSM6035264 r1 GSM6035264 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py MUTANT_S2_L004_I1_001.fastq.gz MUTANT_S2_L004_R1_001.fastq.gz MUTANT_S2_L004_R2_001.fastq.gz fastq fastq fastq 7060634088.0 55595544.0 GSM6035264 r4 0:8 1:28 2:91 A:1337923427;C:1225128065;G:1262793134;T:1229767092;N:3582786 8 28 91   1337923427 1225128065 1262793134 1229767092 3582786 SRX14788266 SRS12547158 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.96323   0.07552   0.84626   0.53808   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69442 69442 SRR18687235 SRX14788265 SRS12547159 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       WT 5mpf scRNA seq GSM6035263   source name:wkm|tissue:marrow|age:5mpf|genotype:WT WT 5mpf scRNA seq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:5mpf|genotype:WT GSM6035263 GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq GSM6035263 r1 GSM6035263 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py WT_S1_L001_I1_001.fastq.gz WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz fastq fastq fastq 7887658469.0 62107547.0 GSM6035263 r1 0:8 1:28 2:91 A:1686084589;C:1207047546;G:1347307215;T:1406353747;N:4993680 8 28 91   1686084589 1207047546 1347307215 1406353747 4993680 SRX14788265 SRS12547159 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.93208   0.13464   0.82885   0.5507   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69443 69443 SRR18687236 SRX14788265 SRS12547159 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       WT 5mpf scRNA seq GSM6035263   source name:wkm|tissue:marrow|age:5mpf|genotype:WT WT 5mpf scRNA seq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:5mpf|genotype:WT GSM6035263 GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq GSM6035263 r1 GSM6035263 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py WT_S1_L002_I1_001.fastq.gz WT_S1_L002_R1_001.fastq.gz WT_S1_L002_R2_001.fastq.gz fastq fastq fastq 7726846751.0 60841313.0 GSM6035263 r2 0:8 1:28 2:91 A:1651285269;C:1182541074;G:1321442374;T:1376689852;N:4600914 8 28 91   1651285269 1182541074 1321442374 1376689852 4600914 SRX14788265 SRS12547159 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.93139   0.13512   0.83157   0.54659   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69444 69444 SRR18687237 SRX14788265 SRS12547159 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       WT 5mpf scRNA seq GSM6035263   source name:wkm|tissue:marrow|age:5mpf|genotype:WT WT 5mpf scRNA seq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:5mpf|genotype:WT GSM6035263 GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq GSM6035263 r1 GSM6035263 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py WT_S1_L003_I1_001.fastq.gz WT_S1_L003_R1_001.fastq.gz WT_S1_L003_R2_001.fastq.gz fastq fastq fastq 7809746382.0 61494066.0 GSM6035263 r3 0:8 1:28 2:91 A:1669649704;C:1195820935;G:1334457445;T:1391506607;N:4525315 8 28 91   1669649704 1195820935 1334457445 1391506607 4525315 SRX14788265 SRS12547159 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.9319   0.13521   0.83039   0.54131   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69445 69445 SRR18687238 SRX14788265 SRS12547159 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       WT 5mpf scRNA seq GSM6035263   source name:wkm|tissue:marrow|age:5mpf|genotype:WT WT 5mpf scRNA seq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:5mpf|genotype:WT GSM6035263 GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq GSM6035263 r1 GSM6035263 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py WT_S1_L004_I1_001.fastq.gz WT_S1_L004_R1_001.fastq.gz WT_S1_L004_R2_001.fastq.gz fastq fastq fastq 7741554113.0 60957119.0 GSM6035263 r4 0:8 1:28 2:91 A:1655590157;C:1185244017;G:1323146581;T:1379127206;N:3989868 8 28 91   1655590157 1185244017 1323146581 1379127206 3989868 SRX14788265 SRS12547159 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.93299   0.13493   0.82852   0.55166   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69446 69446 SRR18687240 SRX14788264 SRS12547155 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       Mutant 12mpf scRNAseq GSM6035262   source name:wkm|tissue:marrow|age:12mpf|genotype:gata2a / Mutant 12mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:12mpf|genotype:gata2a / GSM6035262 GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq GSM6035262 r1 GSM6035262 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py mutant_S2_L001_I1_001.fastq.gz mutant_S2_L001_R1_001.fastq.gz mutant_S2_L001_R2_001.fastq.gz fastq fastq fastq 2802332148.0 21229789.0 GSM6035262 r1 0:8 1:26 2:98 A:640368763;C:436216313;G:577751307;T:426047488;N:135451 8 26 98   640368763 436216313 577751307 426047488 135451 SRX14788264 SRS12547155 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.95554   0.01147   0.92565   0.57239   98   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69447 69447 SRR18687241 SRX14788264 SRS12547155 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       Mutant 12mpf scRNAseq GSM6035262   source name:wkm|tissue:marrow|age:12mpf|genotype:gata2a / Mutant 12mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:12mpf|genotype:gata2a / GSM6035262 GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq GSM6035262 r1 GSM6035262 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py mutant_S2_L002_I1_001.fastq.gz mutant_S2_L002_R1_001.fastq.gz mutant_S2_L002_R2_001.fastq.gz fastq fastq fastq 2716435392.0 20579056.0 GSM6035262 r2 0:8 1:26 2:98 A:630665836;C:423337212;G:549434401;T:413134647;N:175392 8 26 98   630665836 423337212 549434401 413134647 175392 SRX14788264 SRS12547155 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.95616   0.01121   0.92638   0.59372   98   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69448 69448 SRR18687242 SRX14788264 SRS12547155 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       Mutant 12mpf scRNAseq GSM6035262   source name:wkm|tissue:marrow|age:12mpf|genotype:gata2a / Mutant 12mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:12mpf|genotype:gata2a / GSM6035262 GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq GSM6035262 r1 GSM6035262 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py mutant_S2_L003_I1_001.fastq.gz mutant_S2_L003_R1_001.fastq.gz mutant_S2_L003_R2_001.fastq.gz fastq fastq fastq 2866261860.0 21714105.0 GSM6035262 r3 0:8 1:26 2:98 A:662138328;C:448896468;G:581624031;T:434958720;N:364743 8 26 98   662138328 448896468 581624031 434958720 364743 SRX14788264 SRS12547155 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.95475   0.0112   0.9264   0.57664   98   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69449 69449 SRR18687243 SRX14788264 SRS12547155 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       Mutant 12mpf scRNAseq GSM6035262   source name:wkm|tissue:marrow|age:12mpf|genotype:gata2a / Mutant 12mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:12mpf|genotype:gata2a / GSM6035262 GSM6035262: Mutant 12mpf scRNAseq; Danio rerio; RNA Seq GSM6035262 r1 GSM6035262 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py mutant_S2_L004_I1_001.fastq.gz mutant_S2_L004_R1_001.fastq.gz mutant_S2_L004_R2_001.fastq.gz fastq fastq fastq 2778700584.0 21050762.0 GSM6035262 r4 0:8 1:26 2:98 A:646107299;C:435138523;G:558295882;T:423168974;N:263998 8 26 98   646107299 435138523 558295882 423168974 263998 SRX14788264 SRS12547155 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.95523   0.01148   0.92612   0.594   98   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69450 69450 SRR18687249 SRX14788262 SRS12547153 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       WT 12mpf scRNAseq GSM6035261   source name:wkm|tissue:marrow|age:12mpf|genotype:WT WT 12mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:12mpf|genotype:WT GSM6035261 GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq GSM6035261 r1 GSM6035261 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py WT-12mpf_S1_L001_I1_001.fastq.gz WT-12mpf_S1_L001_R1_001.fastq.gz WT-12mpf_S1_L001_R2_001.fastq.gz fastq fastq fastq 2871526284.0 21753987.0 GSM6035261 r1 0:8 1:26 2:98 A:657935861;C:458782361;G:577643976;T:437389248;N:139280 8 26 98   657935861 458782361 577643976 437389248 139280 SRX14788262 SRS12547153 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.95618   0.01409   0.93137   0.57474   98   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69451 69451 SRR18687250 SRX14788262 SRS12547153 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       WT 12mpf scRNAseq GSM6035261   source name:wkm|tissue:marrow|age:12mpf|genotype:WT WT 12mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:12mpf|genotype:WT GSM6035261 GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq GSM6035261 r1 GSM6035261 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py WT-12mpf_S1_L002_I1_001.fastq.gz WT-12mpf_S1_L002_R1_001.fastq.gz WT-12mpf_S1_L002_R2_001.fastq.gz fastq fastq fastq 2786830992.0 21112356.0 GSM6035261 r2 0:8 1:26 2:98 A:646477118;C:445716938;G:552088162;T:424546694;N:181976 8 26 98   646477118 445716938 552088162 424546694 181976 SRX14788262 SRS12547153 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.95703   0.01387   0.93117   0.57965   98   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69452 69452 SRR18687251 SRX14788262 SRS12547153 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       WT 12mpf scRNAseq GSM6035261   source name:wkm|tissue:marrow|age:12mpf|genotype:WT WT 12mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:12mpf|genotype:WT GSM6035261 GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq GSM6035261 r1 GSM6035261 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py WT-12mpf_S1_L003_I1_001.fastq.gz WT-12mpf_S1_L003_R1_001.fastq.gz WT-12mpf_S1_L003_R2_001.fastq.gz fastq fastq fastq 2940233472.0 22274496.0 GSM6035261 r3 0:8 1:26 2:98 A:678078355;C:472082276;G:585591377;T:446774858;N:373742 8 26 98   678078355 472082276 585591377 446774858 373742 SRX14788262 SRS12547153 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.95649   0.01398   0.93237   0.5686   98   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
69453 69453 SRR18687252 SRX14788262 SRS12547153 SRP368307 PRJNA824844 Single cell analysis of zebrafish marrow in WT and gata2a mutant animals GSE200503 Other Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability       WT 12mpf scRNAseq GSM6035261   source name:wkm|tissue:marrow|age:12mpf|genotype:WT WT 12mpf scRNAseq scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly:  GRCz11 wkm cells were not treated 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf tissue:marrow|age:12mpf|genotype:WT GSM6035261 GSM6035261: WT 12mpf scRNAseq; Danio rerio; RNA Seq GSM6035261 r1 GSM6035261 1 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP368307   loader:fastq load.py WT-12mpf_S1_L004_I1_001.fastq.gz WT-12mpf_S1_L004_R1_001.fastq.gz WT-12mpf_S1_L004_R2_001.fastq.gz fastq fastq fastq 2850270720.0 21592960.0 GSM6035261 r4 0:8 1:26 2:98 A:661215163;C:457617537;G:562445244;T:434561966;N:270170 8 26 98   661215163 457617537 562445244 434561966 270170 SRX14788262 SRS12547153 SRA1400926 Institute of Cancer and Genomic Sciences, University of Birminhgam Institute of Cancer and Genomic Sciences, University of Birminhgam 1 0.952   0.0139   0.93188   0.56069   98   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2022-04-08 Adult Adult Marrow Renal System
76638 76638 SRR25247896 SRX20994112 SRS18268519 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow lckmCherry cd79aGFP Population M1 Sample 56 GSM7595977   source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow lckmCherry cd79aGFP Population M1 Sample 56 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA GSM7595977 GSM7595977: Marrow lckmCherry cd79aGFP Population M1 Sample 56; Danio rerio; RNA Seq GSM7595977 r1 GSM7595977 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 56_S68_R1_001.fastq.gz 56_S68_R2_001.fastq.gz fastq fastq 9351083002.0 30963851.0 GSM7595977 r1 0:151 1:151 A:2790598714;C:1668663045;G:1882128783;T:3009655305;N:37155 151 151     2790598714 1668663045 1882128783 3009655305 37155 SRX20994112 SRS18268519 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.71935 0.53678 0.10054 0.10479 0.88895 0.94442 0.71659 0.73656 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76639 76639 SRR25247897 SRX20994111 SRS18268517 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow lckmCherry cd79aGFP Population M1 Sample 55 GSM7595976   source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow lckmCherry cd79aGFP Population M1 Sample 55 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA GSM7595976 GSM7595976: Marrow lckmCherry cd79aGFP Population M1 Sample 55; Danio rerio; RNA Seq GSM7595976 r1 GSM7595976 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 55_S67_R1_001.fastq.gz 55_S67_R2_001.fastq.gz fastq fastq 9888413482.0 32743091.0 GSM7595976 r1 0:151 1:151 A:2884186543;C:1849928947;G:2064604866;T:3089653973;N:39153 151 151     2884186543 1849928947 2064604866 3089653973 39153 SRX20994111 SRS18268517 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.74087 0.57449 0.10781 0.10777 0.88937 0.93768 0.69241 0.41557 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76640 76640 SRR25247898 SRX20994110 SRS18268518 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow lckmCherry cd79aGFP Population M1 Sample 54 GSM7595975   source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow lckmCherry cd79aGFP Population M1 Sample 54 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79aGFP|treatment:NA GSM7595975 GSM7595975: Marrow lckmCherry cd79aGFP Population M1 Sample 54; Danio rerio; RNA Seq GSM7595975 r1 GSM7595975 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 54_S66_R1_001.fastq.gz 54_S66_R2_001.fastq.gz fastq fastq 10451102298.0 34606299.0 GSM7595975 r1 0:151 1:151 A:3121848970;C:1864364809;G:2100878796;T:3363967914;N:41809 151 151     3121848970 1864364809 2100878796 3363967914 41809 SRX20994110 SRS18268518 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.72731 0.54788 0.10584 0.10817 0.88629 0.93941 0.70276 0.71442 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76650 76650 SRR25247908 SRX20994100 SRS18268507 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79aGFP Population M3B Sample 44 GSM7595965   source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79aGFP Population M3B Sample 44 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA GSM7595965 GSM7595965: Marrow rag2RFP cd79aGFP Population M3B Sample 44; Danio rerio; RNA Seq GSM7595965 r1 GSM7595965 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 44_S56_R2_001.fastq.gz 44_S56_R1_001.fastq.gz fastq fastq 9758039176.0 32311388.0 GSM7595965 r1 0:151 1:151 A:2914004460;C:1731748893;G:2001541675;T:3110706309;N:37839 151 151     2914004460 1731748893 2001541675 3110706309 37839 SRX20994100 SRS18268507 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.68224 0.53012 0.15745 0.15669 0.89027 0.93766 0.67516 0.69738 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76651 76651 SRR25247909 SRX20994099 SRS18268506 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79aGFP Population M3B Sample 43 GSM7595964   source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79aGFP Population M3B Sample 43 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA GSM7595964 GSM7595964: Marrow rag2RFP cd79aGFP Population M3B Sample 43; Danio rerio; RNA Seq GSM7595964 r1 GSM7595964 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 43_S55_R1_001.fastq.gz 43_S55_R2_001.fastq.gz fastq fastq 10556595730.0 34955615.0 GSM7595964 r1 0:151 1:151 A:3074035126;C:1954032677;G:2284765668;T:3243720662;N:41597 151 151     3074035126 1954032677 2284765668 3243720662 41597 SRX20994099 SRS18268506 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.69449 0.54884 0.14567 0.14377 0.88485 0.93748 0.68668 0.7032 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76652 76652 SRR25247910 SRX20994098 SRS18268505 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79aGFP Population M3B Sample 42 GSM7595963   source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79aGFP Population M3B Sample 42 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79aGFP|treatment:NA GSM7595963 GSM7595963: Marrow rag2RFP cd79aGFP Population M3B Sample 42; Danio rerio; RNA Seq GSM7595963 r1 GSM7595963 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 42_S54_R2_001.fastq.gz 42_S54_R1_001.fastq.gz fastq fastq 9056440930.0 29988215.0 GSM7595963 r1 0:151 1:151 A:2664832448;C:1675724049;G:1879251595;T:2836597271;N:35567 151 151     2664832448 1675724049 1879251595 2836597271 35567 SRX20994098 SRS18268505 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.74527 0.59162 0.15106 0.16614 0.87527 0.93288 0.67916 0.69017 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76653 76653 SRR25247911 SRX20994097 SRS18268504 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79aGFP Population M3A Sample 41 GSM7595962   source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79aGFP Population M3A Sample 41 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA GSM7595962 GSM7595962: Marrow rag2RFP cd79aGFP Population M3A Sample 41; Danio rerio; RNA Seq GSM7595962 r1 GSM7595962 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 41_S53_R1_001.fastq.gz 41_S53_R2_001.fastq.gz fastq fastq 9203316516.0 30474558.0 GSM7595962 r1 0:151 1:151 A:2725901989;C:1645779996;G:1942649566;T:2888948599;N:36366 151 151     2725901989 1645779996 1942649566 2888948599 36366 SRX20994097 SRS18268504 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.67888 0.52034 0.12258 0.11213 0.86062 0.92468 0.66237 0.68597 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76654 76654 SRR25247912 SRX20994096 SRS18268503 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79aGFP Population M3A Sample 40 GSM7595961   source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79aGFP Population M3A Sample 40 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA GSM7595961 GSM7595961: Marrow rag2RFP cd79aGFP Population M3A Sample 40; Danio rerio; RNA Seq GSM7595961 r1 GSM7595961 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 40_S52_R2_001.fastq.gz 40_S52_R1_001.fastq.gz fastq fastq 9646930054.0 31943477.0 GSM7595961 r1 0:151 1:151 A:2834546007;C:1761986037;G:1973855821;T:3076503975;N:38214 151 151     2834546007 1761986037 1973855821 3076503975 38214 SRX20994096 SRS18268503 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.76551 0.60892 0.13414 0.13895 0.86048 0.9207 0.65791 0.67293 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76655 76655 SRR25247913 SRX20994095 SRS18268502 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79aGFP Population M3A Sample 39 GSM7595960   source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79aGFP Population M3A Sample 39 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79aGFP|treatment:NA GSM7595960 GSM7595960: Marrow rag2RFP cd79aGFP Population M3A Sample 39; Danio rerio; RNA Seq GSM7595960 r1 GSM7595960 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 39_S51_R1_001.fastq.gz 39_S51_R2_001.fastq.gz fastq fastq 8440558740.0 27948870.0 GSM7595960 r1 0:151 1:151 A:2490529515;C:1538128719;G:1758588428;T:2653278666;N:33412 151 151     2490529515 1538128719 1758588428 2653278666 33412 SRX20994095 SRS18268502 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.74478 0.59902 0.13437 0.14723 0.86663 0.92616 0.65496 0.6824 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76656 76656 SRR25247914 SRX20994094 SRS18268501 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79aGFP Population M1 Sample 36 GSM7595959   source name:Marrow|tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79aGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79aGFP Population M1 Sample 36 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79aGFP|treatment:NA GSM7595959 GSM7595959: Marrow rag2RFP cd79aGFP Population M1 Sample 36; Danio rerio; RNA Seq GSM7595959 r1 GSM7595959 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 36_S48_R1_001.fastq.gz 36_S48_R2_001.fastq.gz fastq fastq 8449201376.0 27977488.0 GSM7595959 r1 0:151 1:151 A:2435565387;C:1600925575;G:1814354263;T:2598322866;N:33285 151 151     2435565387 1600925575 1814354263 2598322866 33285 SRX20994094 SRS18268501 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.68458 0.50808 0.15645 0.14862 0.88067 0.93385 0.67951 0.69099 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76669 76669 SRR25247926 SRX20994081 SRS18268488 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow lckmCherry cd79bGFP Population M1 Sample 23 GSM7595946   source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow lckmCherry cd79bGFP Population M1 Sample 23 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA GSM7595946 GSM7595946: Marrow lckmCherry cd79bGFP Population M1 Sample 23; Danio rerio; RNA Seq GSM7595946 r1 GSM7595946 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 23_S35_R1_001.fastq.gz 23_S35_R2_001.fastq.gz fastq fastq 9087292344.0 30090372.0 GSM7595946 r1 0:151 1:151 A:2696974908;C:1687411669;G:1887706429;T:2815163605;N:35733 151 151     2696974908 1687411669 1887706429 2815163605 35733 SRX20994081 SRS18268488 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.6653 0.45253 0.10733 0.09681 0.90806 0.94935 0.72764 0.73406 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76670 76670 SRR25247927 SRX20994080 SRS18268487 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow lckmCherry cd79bGFP Population M1 Sample 22 GSM7595945   source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow lckmCherry cd79bGFP Population M1 Sample 22 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA GSM7595945 GSM7595945: Marrow lckmCherry cd79bGFP Population M1 Sample 22; Danio rerio; RNA Seq GSM7595945 r1 GSM7595945 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 22_S34_R1_001.fastq.gz 22_S34_R2_001.fastq.gz fastq fastq 9623138796.0 31864698.0 GSM7595945 r1 0:151 1:151 A:2754394984;C:1823594508;G:2149500970;T:2895610034;N:38300 151 151     2754394984 1823594508 2149500970 2895610034 38300 SRX20994080 SRS18268487 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.47113 0.29499 0.09705 0.06858 0.94095 0.96349 0.70694 0.72308 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76671 76671 SRR25247929 SRX20994079 SRS18268486 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow lckmCherry cd79bGFP Population M1 Sample 21 GSM7595944   source name:Marrow|tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow lckmCherry cd79bGFP Population M1 Sample 21 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:Early T committed|genotype:lckmCherry cd79bGFP|treatment:NA GSM7595944 GSM7595944: Marrow lckmCherry cd79bGFP Population M1 Sample 21; Danio rerio; RNA Seq GSM7595944 r1 GSM7595944 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 21_S33_R2_001.fastq.gz 21_S33_R1_001.fastq.gz fastq fastq 7877331458.0 26083879.0 GSM7595944 r1 0:151 1:151 A:2282670114;C:1496631823;G:1685330538;T:2412668409;N:30574 151 151     2282670114 1496631823 1685330538 2412668409 30574 SRX20994079 SRS18268486 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.59088 0.41604 0.11324 0.09655 0.93685 0.95692 0.67515 0.72761 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76674 76674 SRR25247932 SRX20994076 SRS18268483 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M4 Sample 18 GSM7595941   source name:Marrow|tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M4 Sample 18 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595941 GSM7595941: Marrow rag2RFP cd79bGFP Population M4 Sample 18; Danio rerio; RNA Seq GSM7595941 r1 GSM7595941 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 18_S30_R1_001.fastq.gz 18_S30_R2_001.fastq.gz fastq fastq 9378458396.0 31054498.0 GSM7595941 r1 0:151 1:151 A:2719764060;C:1763237221;G:1999860307;T:2895559786;N:37022 151 151     2719764060 1763237221 1999860307 2895559786 37022 SRX20994076 SRS18268483 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.75321 0.57729 0.14283 0.15696 0.89708 0.94296 0.72648 0.40661 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76675 76675 SRR25247936 SRX20994075 SRS18268482 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M4 Sample 17 GSM7595940   source name:Marrow|tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M4 Sample 17 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595940 GSM7595940: Marrow rag2RFP cd79bGFP Population M4 Sample 17; Danio rerio; RNA Seq GSM7595940 r1 GSM7595940 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 17_S29_R1_001.fastq.gz 17_S29_R2_001.fastq.gz fastq fastq 8603160674.0 28487287.0 GSM7595940 r1 0:151 1:151 A:2487183090;C:1628390382;G:1810834659;T:2676718560;N:33983 151 151     2487183090 1628390382 1810834659 2676718560 33983 SRX20994075 SRS18268482 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.75738 0.57611 0.12217 0.12508 0.8898 0.93943 0.68863 0.39147 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76676 76676 SRR25247933 SRX20994074 SRS18268481 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M4 Sample 16 GSM7595939   source name:Marrow|tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M4 Sample 16 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage III|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595939 GSM7595939: Marrow rag2RFP cd79bGFP Population M4 Sample 16; Danio rerio; RNA Seq GSM7595939 r1 GSM7595939 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 16_S28_R1_001.fastq.gz 16_S28_R2_001.fastq.gz fastq fastq 12335217784.0 40845092.0 GSM7595939 r1 0:151 1:151 A:3615039679;C:2300903967;G:2575715695;T:3843509545;N:48898 151 151     3615039679 2300903967 2575715695 3843509545 48898 SRX20994074 SRS18268481 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.68959 0.50352 0.1172 0.10233 0.90352 0.94537 0.72822 0.74253 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76677 76677 SRR25247934 SRX20994073 SRS18268480 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M3B Sample 15 GSM7595938   source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M3B Sample 15 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595938 GSM7595938: Marrow rag2RFP cd79bGFP Population M3B Sample 15; Danio rerio; RNA Seq GSM7595938 r1 GSM7595938 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 15_S27_R1_001.fastq.gz 15_S27_R2_001.fastq.gz fastq fastq 8202696594.0 27161247.0 GSM7595938 r1 0:151 1:151 A:2344172206;C:1580848264;G:1802238700;T:2475405027;N:32397 151 151     2344172206 1580848264 1802238700 2475405027 32397 SRX20994073 SRS18268480 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.63815 0.43487 0.08008 0.06825 0.90218 0.94483 0.65063 0.66839 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76678 76678 SRR25247935 SRX20994072 SRS18268478 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M3B Sample 14 GSM7595937   source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M3B Sample 14 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595937 GSM7595937: Marrow rag2RFP cd79bGFP Population M3B Sample 14; Danio rerio; RNA Seq GSM7595937 r1 GSM7595937 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 14_S26_R2_001.fastq.gz 14_S26_R1_001.fastq.gz fastq fastq 7915147294.0 26209097.0 GSM7595937 r1 0:151 1:151 A:2265670905;C:1520031310;G:1849059138;T:2280354641;N:31300 151 151     2265670905 1520031310 1849059138 2280354641 31300 SRX20994072 SRS18268478 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.53533 0.39855 0.13942 0.1317 0.9151 0.94714 0.6754 0.68314 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76679 76679 SRR25247937 SRX20994071 SRS18268479 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M3B Sample 13 GSM7595936   source name:Marrow|tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M3B Sample 13 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage II|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595936 GSM7595936: Marrow rag2RFP cd79bGFP Population M3B Sample 13; Danio rerio; RNA Seq GSM7595936 r1 GSM7595936 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 13_S25_R1_001.fastq.gz 13_S25_R2_001.fastq.gz fastq fastq 9721695892.0 32191046.0 GSM7595936 r1 0:151 1:151 A:2858891195;C:1802515744;G:2029257538;T:3030992999;N:38416 151 151     2858891195 1802515744 2029257538 3030992999 38416 SRX20994071 SRS18268479 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.76749 0.60878 0.1349 0.15464 0.87604 0.93365 0.67533 0.65373 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76680 76680 SRR25247938 SRX20994070 SRS18268477 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M3A Sample 12 GSM7595935   source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M3A Sample 12 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595935 GSM7595935: Marrow rag2RFP cd79bGFP Population M3A Sample 12; Danio rerio; RNA Seq GSM7595935 r1 GSM7595935 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 12_S24_R1_001.fastq.gz 12_S24_R2_001.fastq.gz fastq fastq 8731763750.0 28913125.0 GSM7595935 r1 0:151 1:151 A:2551441984;C:1639877964;G:1850759915;T:2689649693;N:34194 151 151     2551441984 1639877964 1850759915 2689649693 34194 SRX20994070 SRS18268477 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.74961 0.60373 0.12646 0.15649 0.87487 0.93332 0.6854 0.70294 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76681 76681 SRR25247939 SRX20994069 SRS18268476 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M3A Sample 11 GSM7595934   source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M3A Sample 11 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595934 GSM7595934: Marrow rag2RFP cd79bGFP Population M3A Sample 11; Danio rerio; RNA Seq GSM7595934 r1 GSM7595934 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 11_S23_R1_001.fastq.gz 11_S23_R2_001.fastq.gz fastq fastq 8131157626.0 26924363.0 GSM7595934 r1 0:151 1:151 A:2378241179;C:1520823030;G:1694205993;T:2537855107;N:32317 151 151     2378241179 1520823030 1694205993 2537855107 32317 SRX20994069 SRS18268476 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.7694 0.58873 0.12189 0.13976 0.87432 0.93332 0.6609 0.68659 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76682 76682 SRR25247940 SRX20994068 SRS18268475 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M3A Sample 10 GSM7595933   source name:Marrow|tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M3A Sample 10 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:B Stage I|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595933 GSM7595933: Marrow rag2RFP cd79bGFP Population M3A Sample 10; Danio rerio; RNA Seq GSM7595933 r1 GSM7595933 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 10_S22_R1_001.fastq.gz 10_S22_R2_001.fastq.gz fastq fastq 8963294466.0 29679783.0 GSM7595933 r1 0:151 1:151 A:2619732708;C:1669568274;G:1858403783;T:2815553963;N:35738 151 151     2619732708 1669568274 1858403783 2815553963 35738 SRX20994068 SRS18268475 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.77821 0.60379 0.10495 0.12779 0.86825 0.92492 0.62624 0.60864 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76683 76683 SRR25247944 SRX20994067 SRS18268474 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M1 Sample 8 GSM7595932   source name:Marrow|tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M1 Sample 8 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595932 GSM7595932: Marrow rag2RFP cd79bGFP Population M1 Sample 8; Danio rerio; RNA Seq GSM7595932 r1 GSM7595932 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 8_S20_R1_001.fastq.gz 8_S20_R2_001.fastq.gz fastq fastq 9142544452.0 30273326.0 GSM7595932 r1 0:151 1:151 A:2630198533;C:1744556837;G:1930871463;T:2836881708;N:35911 151 151     2630198533 1744556837 1930871463 2836881708 35911 SRX20994067 SRS18268474 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.7212 0.52336 0.12114 0.1298 0.89929 0.94259 0.67128 0.68712 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System
76684 76684 SRR25247941 SRX20994066 SRS18268473 SRP448831 PRJNA994052 Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model GSE237139 Transcriptome Analysis The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…   pubmed:38656392   Marrow rag2RFP cd79bGFP Population M1 Sample 7 GSM7595931   source name:Marrow|tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79bGFP|treatment:NA|geo loc name:missing|collection date:missing Marrow rag2RFP cd79bGFP Population M1 Sample 7 Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample Marrow   Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols. For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. tissue:Marrow|cell type:Early B committed|genotype:rag2RFP cd79bGFP|treatment:NA GSM7595931 GSM7595931: Marrow rag2RFP cd79bGFP Population M1 Sample 7; Danio rerio; RNA Seq GSM7595931 r1 GSM7595931 1 Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448831   loader:fastq load.py 7_S19_R1_001.fastq.gz 7_S19_R2_001.fastq.gz fastq fastq 7906272118.0 26179709.0 GSM7595931 r1 0:151 1:151 A:2254838087;C:1527167803;G:1677900707;T:2446333840;N:31681 151 151     2254838087 1527167803 1677900707 2446333840 31681 SRX20994066 SRS18268473 SRA1671790 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 2 0.72774 0.52811 0.10506 0.09722 0.90443 0.94339 0.65125 0.68364 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   United States 2023-07-12 Undetermined Undetermined Marrow Renal System

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