run_metadata: 29813
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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| 29813 | SRR27466772 | SRX23138319 | SRS20089385 | SRP482605 | PRJNA1062705 | Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation | GSE252788 | Transcriptome Analysis | Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized which limits their applicability to studying human disease. Here we show by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors including C/ebp ß which is important for late neutrophil maturation. Cross species comparison of zebrafish mouse and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult six mpf male zebrafish was isolated labelled using lipid tagged following MULTI seq protocol for scRNA seq using 10x Genomics. | pubmed:38413586 | MF317 A2 GEX zebrafish multiseq | GSM8007850 | source name:Kidney marrow|tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs|geo loc name:missing|collection date:missing | MF317 A2 GEX zebrafish multiseq | We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object | Kidney marrow | Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer’s protocols 10x Genomics and sequenced by protocol. | tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs | GSM8007850 | GSM8007850: MF317 A2 GEX zebrafish multiseq; Danio rerio; RNA Seq | GSM8007850 r1 | GSM8007850 | 1 | Each kidney marrow was split into four portions labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO INT HI or WKM. All cells were gated on live gate for WKM debris was excluded in a FSC/SSC gate and mmp9 NO INT HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics Pleasanton CA according to the manufacturer's protocols 10x Genomics and sequenced by protocol. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP482605 | loader:fastq load.py | MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_I1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R2_001.fastq.gz | fastq fastq fastq | 609557670.0 | 4515242.0 | GSM8007850 r2 | 0:8 1:29 2:98 | A:288037892;C:47138905;G:85961330;T:21289087;N:66502 | 8 | 29 | 98 | 288037892 | 47138905 | 85961330 | 21289087 | 66502 | SRX23138319 | SRS20089385 | Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI) | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Austria | 2024-01-09 | Undetermined | Adult | Multi-tissue | Multi-system |