run_metadata: 62678
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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| 62678 | SRR13302564 | SRX9731496 | SRS7924278 | SRP299270 | PRJNA687691 | The alx3 gene functions to regulate skeletal cell differentiation timing during zebrafish neurocranium development. | GSE163826 | Other | During craniofacial development different populations of cartilage and bone forming cells develop in precise locations in the head. Most of these cells are derived from pluripotent cranial neural crest cells. The mechanisms that divide neural crest cells into distinct populations are not fully understood. Here we use single cell RNA sequencing to transcriptomically define different populations of cranial neural crest cells. We discovered that the transcription factor encoding alx gene family is restricted to the frontonasal population of neural crest cells. Furthermore genetic mutant analyses indicate that alx3 functions to subdivide the frontonasal population into medial versus lateral subpopulations. Our results support a mechanism in which the alx gene family functions as an identity code subdividing frontonasal neural crest cells into distinct subpopulations. This study furthers our understanding of how different skeletal cell fates are established during craniofacial development and how these mechanisms can go awry in genetic diseases. Overall design: neural crest cell profiling of 24 hpf WT D. rerio | pubmed:33741714;pubmed:36134886 | WT rep 1 | GSM4988014 | tissue:Nerual crest cells|tissue source:neuroectoderm|strain:AB strain|age:24 hpf | WT rep 1 | make ref / make fastq files / aggr command / count command; CellRanger 2.2.0 merge WT and mut data; Seurat v2; e10x < MergeSeuratobject1 = wt object2 = mut project = "n10x" min.cells = 5 min.genes = 100 filter for <250 genes per cell and for any mitochondrial UMIs at less than or equal to 2.5% per cell; Seurat v2; e10x < FilterCellsobject = e10x subset.names = c"nGene" "percent.mito" low.thresholds = c250 Inf high.thresholds = cInf 0.025 cluster projection/dim red. Via PCA/UMAP post WT subset; Seurat v2; nichols TSNE < RunTSNEnichols dr seurat WT dims.use = 1:10 do.fast= TRUE seed.use = 123/nichols umap clusters < FindClustersobject = nichols TSNE reduction.type = "pca" dims.use = 1:15 resolution = 0.2 save.SNN = TRUE n.start = 10 nn.eps = 0.5 print.output = FALSE force.recalc = TRUE/nichols umap clusters < FindClustersobject = nichols TSNE reduction.type = "pca" dims.use = 1:15 resolution = 0.2 save.SNN = TRUE n.start = 10 nn.eps = 0.5 print.output = FALSE force.recalc = TRUE main dim reduction plot; Seurat v2; DimPlotobject = nichols umap clusters reduction.use = "umap" do.return = TRUE pt.size = 1.3 differential expression marker gene ID/localization of expression; Seurat v2; nichols umap.markers1 < FindAllMarkersnichols umap clusters only.pos = TRUE min.pct = 0.1 thresh.use = 0.25/FeaturePlot organizing genes by descending ascending pct.2; Seurat v2; subset based on ascending pct.2 visualize distribution of alx genes across each cluster; Seurat v2; VlnPlotnichols umap clusters features.plot = <each alx gene> single.legend = TRUE y.max = 2 + ggplot2::theme classic + ylab"Expression Level log TPM" pseudotemporal and lineage tracing analyses; mnonocle3 v3; Follows from pseudotime and lineage trajectory mapping vignette for Monocle 3 Trapnell et al. 2014 seurat /featureplot app; Seurat v2 RShiny; FeaturePlotnichols umap clusters diet features = input$gene name reduction = "umap" cols = c"grey" "blue" label = TRUE label.size = 4.5 pt.size = 1.5 ncol = 3 + xlim 10 10 + ylim 10 15; used the diet seurat function native to seurat to generate the "skiny" object used here lineage tracing/trajectory analysis app; monocle3 v3 Rshiny; plot cellsNichols cds subset genes = input$gene name cell size = 1.5 graph label size = 3 group label size = 4 + themeplot.title = element textsize = 25; uses the main cell data set object as in our pseudotemporal and lineage tracing analyses Genome build: GRCz11/danRer11 Supplementary files format and content: counts.csv Supplementary files format and content: raw UMI counts per gene per cell | Nerual crest cells | Crispr/cas9 mutagenesis of alx3 gene Jao et al. 2013 Barske et al. 2016 | 32 double transgenic flia:EGFP;sox10:mRFP embryos were dissociated into single cell suspension using cold active protease from Bacillus licheniformis DNase EDTA and trituration Adam et al. 2017 10X Genomics libraries | Animals were maintained and staged according to established protocols Westerfield 1993 Kimmel et al. 1995. | tissue source:neuroectoderm|strain:AB strain|age:24 hpf | GSM4988014 | GSM4988014: WT rep 1; Danio rerio; RNA Seq | GSM4988014 | 1 | 32 double transgenic flia:EGFP;sox10:mRFP embryos were dissociated into single cell suspension using cold active protease from Bacillus licheniformis DNase EDTA and trituration Adam et al. 2017 10X Genomics libraries | GEO Accession:GSM4988014 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP299270 | 2_mef_wt_High_24hpf_R1_001.fastq.gz 2_mef_wt_High_24hpf_R2_001.fastq.gz | fastq fastq | 233119629204.0 | 771919302.0 | GSM4988014 r1 | 0:151 1:151 | A:69457580771;C:37624255978;G:33980317215;T:87522302829;N:4535172411 | 151 | 151 | 69457580771 | 37624255978 | 33980317215 | 87522302829 | 4535172411 | SRX9731496 | SRS7924278 | SRA1177732 | GEO | Nichols Lab, Craniofacial Biology, University of Colorado - Anschutz Medical Campus | 2 | 0.05174 | 0.87764 | 0.00382 | 0.06802 | 0.98435 | 0.84443 | 0.4489 | 0.49905 | 151 | 151 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-12-24 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures |