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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
74804 SRR24043073 SRX19845029 SRS17204126 SRP430482 PRJNA951388 single cell RNA sequencing analysis of metaphocytes and epidermal cells GSE228737 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes we performed single cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells from the epidemris of 6 mpf Tgspic:EGFP fish parent bioproject:PRJNA951389 pubmed:37148242   epi2 GSM7135751   source name:epidermis|tissue:epidermis|development stage:6 mpf|cell type:spic:EGFP+ and singlet cells|strain:Tgspic:EGFP|genotype:WT epi2 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. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files epidermis   Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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:epidermis|development stage:6 mpf|cell type:spic:EGFP+ and singlet cells|strain:Tgspic:EGFP|genotype:WT GSM7135751 GSM7135751: epi2; Danio rerio; RNA Seq GSM7135751 r1 GSM7135751 1 Six adult Tgspic:EGFP fish were sacrificed 8 000 EGFP+ cells and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. 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   SRP430482     epi2_S1_L001_R1_001.fastq.gz epi2_S1_L001_R2_001.fastq.gz fastq fastq 53272554600.0 177575182.0 GSM7135751 r1 0:150 1:150 A:22273594251;C:9171565164;G:8634752690;T:13192111379;N:531116 150 150     22273594251 9171565164 8634752690 13192111379 531116 SRX19845029 SRS17204126 SRA1614473 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.0 0.87992 0.0 0.19142 1.0 0.8143   0.56327 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-04-02 Adult Adult Skin Surface Structure