{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.library_source = \"TRANSCRIPTOMIC\" and tissue_curation = \"Marrow\"", "rows": [[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", null, "scRNA seq gata2b ko 3", "GSM4568915", null, "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 \u03bcm 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", null, "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 \u03bcm 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. 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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", null, "scRNA seq gata2b ko 2", "GSM4568914", null, "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 \u03bcm 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", null, "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 \u03bcm 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. 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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", null, "scRNA seq gata2b ko 1", "GSM4568913", null, "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 \u03bcm 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", null, "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 \u03bcm 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. 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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", null, "scRNA seq gata2b het 3", "GSM4568912", null, "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 \u03bcm 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", null, "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 \u03bcm 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", null, "SRP264841", null, "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, null, null, null, 1054965741, 827475497, 744430159, 1069699165, 15827, "SRX8402004", "SRS6714761", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.89246, null, 0.06392, null, 0.83934, null, 0.56422, null, 58, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [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", null, "scRNA seq gata2b het 2", "GSM4568911", null, "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 \u03bcm 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", null, "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 \u03bcm 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", null, "SRP264841", null, "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, null, null, null, 1490260317, 1191725100, 1122517464, 1553457613, 14489, "SRX8402003", "SRS6714760", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.90302, null, 0.07865, null, 0.82603, null, 0.57406, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [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", null, "scRNA seq gata2b het 1", "GSM4568910", null, "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 \u03bcm 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", null, "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 \u03bcm 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", null, "SRP264841", null, "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, null, null, null, 1307674780, 1043797904, 1001646002, 1348693620, 19498, "SRX8402002", "SRS6714759", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.90603, null, 0.07667, null, 0.82704, null, 0.57543, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [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", null, "scRNA seq wildtype 3", "GSM4568909", null, "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 \u03bcm 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", null, "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 \u03bcm 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", null, "SRP264841", null, "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, null, null, null, 955572407, 728586737, 678902164, 985710022, 14356, "SRX8402001", "SRS6714758", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.88271, null, 0.06967, null, 0.8284, null, 0.54728, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [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", null, "scRNA seq wildtype 2", "GSM4568908", null, "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 \u03bcm 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", null, "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 \u03bcm 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", null, "SRP264841", null, "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, null, null, null, 1040969741, 863166087, 810647668, 1098105772, 9986, "SRX8402000", "SRS6714757", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.91023, null, 0.06938, null, 0.83238, null, 0.54799, null, 59, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [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", null, "scRNA seq wildtype 1", "GSM4568907", null, "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 \u03bcm 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", null, "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 \u03bcm 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", null, "SRP264841", null, "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, null, null, null, 1040800033, 822608649, 765542043, 1046781383, 15983, "SRX8401999", "SRS6714756", "SRA1080050", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.8978, null, 0.05341, null, 0.84167, null, 0.59389, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2020-05-26", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "Mutant 5mpf scRNAseq", "GSM6035264", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.07511, null, 0.84861, null, 0.53711, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "Mutant 5mpf scRNAseq", "GSM6035264", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.07559, null, 0.84869, null, 0.53571, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "Mutant 5mpf scRNAseq", "GSM6035264", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.07544, null, 0.84776, null, 0.54532, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "Mutant 5mpf scRNAseq", "GSM6035264", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.07552, null, 0.84626, null, 0.53808, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "WT 5mpf scRNA seq", "GSM6035263", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.13464, null, 0.82885, null, 0.5507, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "WT 5mpf scRNA seq", "GSM6035263", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.13512, null, 0.83157, null, 0.54659, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "WT 5mpf scRNA seq", "GSM6035263", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.13521, null, 0.83039, null, 0.54131, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "WT 5mpf scRNA seq", "GSM6035263", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.13493, null, 0.82852, null, 0.55166, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "Mutant 12mpf scRNAseq", "GSM6035262", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.01147, null, 0.92565, null, 0.57239, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "Mutant 12mpf scRNAseq", "GSM6035262", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.01121, null, 0.92638, null, 0.59372, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "Mutant 12mpf scRNAseq", "GSM6035262", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.0112, null, 0.9264, null, 0.57664, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "Mutant 12mpf scRNAseq", "GSM6035262", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.01148, null, 0.92612, null, 0.594, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "WT 12mpf scRNAseq", "GSM6035261", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.01409, null, 0.93137, null, 0.57474, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "WT 12mpf scRNAseq", "GSM6035261", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.01387, null, 0.93117, null, 0.57965, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "WT 12mpf scRNAseq", "GSM6035261", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.01398, null, 0.93237, null, 0.5686, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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", null, null, null, "WT 12mpf scRNAseq", "GSM6035261", null, "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: \u00a0GRCz11", "wkm", "cells were not treated", "10x genomics microfluidics system was used to isolate cells 3\u2019 scRNAseq was completed using Chromium Next GEM single cell 3\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP368307", null, "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, null, 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, null, 0.0139, null, 0.93188, null, 0.56069, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2022-04-08", "Adult", "Adult", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  lckmCherry cd79aGFP  Population M1  Sample 56", "GSM7595977", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  lckmCherry cd79aGFP  Population M1  Sample 55", "GSM7595976", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  lckmCherry cd79aGFP  Population M1  Sample 54", "GSM7595975", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79aGFP  Population M3B  Sample 44", "GSM7595965", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79aGFP  Population M3B  Sample 43", "GSM7595964", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79aGFP  Population M3B  Sample 42", "GSM7595963", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79aGFP  Population M3A  Sample 41", "GSM7595962", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79aGFP  Population M3A  Sample 40", "GSM7595961", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79aGFP  Population M3A  Sample 39", "GSM7595960", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79aGFP  Population M1  Sample 36", "GSM7595959", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  lckmCherry cd79bGFP  Population M1  Sample 23", "GSM7595946", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  lckmCherry cd79bGFP  Population M1  Sample 22", "GSM7595945", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  lckmCherry cd79bGFP  Population M1  Sample 21", "GSM7595944", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M4  Sample 18", "GSM7595941", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M4  Sample 17", "GSM7595940", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M4  Sample 16", "GSM7595939", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M3B  Sample 15", "GSM7595938", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M3B  Sample 14", "GSM7595937", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M3B  Sample 13", "GSM7595936", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M3A  Sample 12", "GSM7595935", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M3A  Sample 11", "GSM7595934", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M3A  Sample 10", "GSM7595933", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M1  Sample 8", "GSM7595932", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"], [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 \u00d7 cd79a:GFP  rag2:RFP \u00d7 cd79b:GFP  cd79a:GFP \u00d7 lck:mCherry  and cd79b:GFP \u00d7 lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcriptomic analysis.", null, "pubmed:38656392", null, "Marrow  rag2RFP cd79bGFP  Population M1  Sample 7", "GSM7595931", null, "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", null, "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\u2019 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448831", null, "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, null, null, 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", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "Marrow", "Renal System"]], "truncated": false, "filtered_table_rows_count": 49, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", 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