run_metadata: 74859
This data as json
| 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 |
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| 74859 | SRR24049048 | SRX19850770 | SRS17208527 | SRP430632 | PRJNA951670 | Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs | GSE228806 | Transcriptome Analysis | Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity tissue regeneration and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures respectively as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties. Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis gill intestine liver heart and brain of 6 mpf Tgmpeg1.1:DsRedx fish | pubmed:37453064 | intestine | GSM7139011 | source name:intestine|tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing | intestine | Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files | intestine | For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell. | tissue:intestine|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT | GSM7139011 | GSM7139011: intestine; Danio rerio; RNA Seq | GSM7139011 r1 | GSM7139011 | 1 | For each organ six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief post the cell sorting single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP430632 | intestine_S1_L004_R1_001.fastq.gz intestine_S1_L004_R2_001.fastq.gz | fastq fastq | 54717610800.0 | 182392036.0 | GSM7139011 r4 | 0:150 1:150 | A:22673425061;C:9440232860;G:8902374859;T:13701032682;N:545338 | 150 | 150 | 22673425061 | 9440232860 | 8902374859 | 13701032682 | 545338 | SRX19850770 | SRS17208527 | SRA1615101 | Room 6319, Division of Life Science, Hong Kong University of Science and Technology | Room 6319, Division of Life Science, Hong Kong University of Science and Technology | 2 | 0.0 | 0.88623 | 0.0 | 0.17703 | 1.0 | 0.82004 | 0.57688 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-04-03 | Adult | Adult | Gut | Digestive System |