{"database": "metadata", "table": "run_metadata", "rows": [[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"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["59305"], "units": {}, "query_ms": 10.47191499674227}