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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
66734 SRR16518315 SRX12721080 SRS10670483 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.   pubmed:35759948   Ac LDL hi 1 GSM5643373   source name:sinusoids|tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:sinusoids Ac LDL hi 1 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. Genome build: GRCz11 Supplementary files format and content: Tags per million TPM values for each sample. sinusoids   Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing 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’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing 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 the Nextera XT DNA Library Preparation Kit illumina.   tissue:Sorted from the kidney|age:adult|genotype:wild type|cell type:sinusoids GSM5643373 GSM5643373: Ac LDL hi 1; Danio rerio; RNA Seq GSM5643373 r1 GSM5643373 1 Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using the RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer containing 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 synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer containing oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer to amplify small size DNA containing 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 the Nextera XT DNA Library Preparation Kit illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP342508     Ac-LDL-hi-1_1.fq.gz Ac-LDL-hi-1_2.fq.gz fastq fastq 5352974400.0 17843248.0 GSM5643373 r1 0:150 1:150 A:1359148172;C:1231019883;G:1385606834;T:1377113418;N:86093 150 150     1359148172 1231019883 1385606834 1377113418 86093 SRX12721080 SRS10670483 SRA1524642 Kanazawa University Kanazawa University 2 0.94458 0.94286 0.09932 0.10018 0.74789 0.75006 0.48096 0.48099 150 150 B B biological fallback assumption illumina nextseq 3prime poly_a nextera sc single_cell_plate quartzseq   Japan 2021-10-21 Adult Adult Kidney Renal System