run_metadata: 24755
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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 |
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| 24755 | SRR25492060 | SRX21223181 | SRS18479984 | SRP452960 | PRJNA1001330 | Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish | GSE239880 | Transcriptome Analysis | The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq. | KBTRE normal replicate S3 | GSM7676122 | source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing | KBTRE normal replicate S3 | Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files | whole embryo | For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR. | tissue:whole embryo|cell type:neutrophils | GSM7676122 | GSM7676122: KBTRE normal replicate S3; Danio rerio; RNA Seq | GSM7676122 r1 | GSM7676122 | 1 | For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP452960 | loader:fastq load.py | HYWGVBCXY_KBTREnormal_S3_L001_I1_001.fastq.gz HYWGVBCXY_KBTREnormal_S3_L001_R1_001.fastq.gz HYWGVBCXY_KBTREnormal_S3_L001_R2_001.fastq.gz | fastq fastq fastq | 601191756.0 | 4554483.0 | GSM7676122 r4 | 0:8 1:26 2:98 | A:127796557;C:93739084;G:103899258;T:120809536;N:94899 | 8 | 26 | 98 | 127796557 | 93739084 | 103899258 | 120809536 | 94899 | SRX21223181 | SRS18479984 | SRA1685258 | Facultad de Ciencias de la vida, Universidad Andres Bello | Facultad de Ciencias de la vida, Universidad Andres Bello | 1 | 0.92144 | 0.08536 | 0.85328 | 0.47066 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Chile | 2023-08-02 | Undetermined | Embryo | Whole Organism | All anatomical structures |