{"database": "metadata", "table": "run_metadata", "rows": [[66739, "SRR19117214", "SRX15184903", "SRS12924346", "SRP342508", "PRJNA773247", "Gene expression analysis of hematopoietic niche cells in the zebrafish kidney", "GSE186298", "Transcriptome Analysis", "The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover  transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney  termed the \"kidney marrow\"  providing an attractive tool for studying hematopoietic niches. Here  we isolated two candidate niche cell populations from the zebrafish kidney  pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low density lipoprotein Ac LDL  whereas pericytes can be labeled by pdgfrb expression. Therefore  pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488 conjugated Ac LDL  respectively. In addition  we also utilized a cell line generated from the zebrafish kidney  zebrafish kidney stromal ZKS  which have been shown to support proliferation of various hematopoietic precursors Stachula et al.  2009. In this study  we performed RNA seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ DP hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells DP uncul  gata2a+ runx1+ cells co cultured with ZKS cells DP cocul  and gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo DP IW+Th. Overall design: mRNA profiles of isolated ZKS cells  pericytes  sinusoids  and gata2a+ runx1+ DP in the zebrafish kidney were generated by Quartz seq using Illumina NextSeq500.", null, "pubmed:35759948", null, "DP IW+Th 2", "GSM6111983", null, "source name:gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo|tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo", "DP IW+Th 2", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Tags per million TPM were calculated using the Subread ver. 1.6.4. Assembly: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample.", "gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo", null, "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3\u2019 ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "tissue:Sorted from the kidney|age:adult|genotype:wild type|treatment:gata2a+ runx1+ cells co cultured with ZKS cells in the presence of both IWR 1 endo and Thpo", "GSM6111983", "GSM6111983: DP IW+Th 2; Danio rerio; RNA Seq", "GSM6111983 r1", "GSM6111983", "1", "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP342508", null, "loader:fastq load.py", "DP_IW+Th_2_L1_1.fq.gz DP_IW+Th_2_L1_2.fq.gz", "fastq fastq", 8969949600.0, 29899832.0, "GSM6111983 r1", "0:150 1:150", "A:2214657919;C:2139450844;G:2332885774;T:2282841671;N:113392", 150, 150, null, null, 2214657919, 2139450844, 2332885774, 2282841671, 113392, "SRX15184903", "SRS12924346", "SRA1415793", "Kanazawa University", "Kanazawa University", 2, 0.91433, 0.91342, 0.11652, 0.11712, 0.87765, 0.87817, 0.46807, 0.47014, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "nextera", "sc", "single_cell_plate", "quartzseq", null, "Japan", "2022-05-06", "Adult", "Adult", "Kidney", "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": ["66739"], "units": {}, "query_ms": 11.703436000971124}