EEL Mouse 440 genes single cell data

<strong>Cell by gene matrix of the EEL mouse 440 gene experiment.</strong> Single cell data generated by EEL FISH on a saggital mouse brain section. The dataset is available in 3 file formats: .loom Loom file see: http://loompy.org/ .h5ad AnnData file see: https://anndata.readthedocs.io/en/latest/index.html .tab Tab-delimited file. <strong>Metadata</strong> Age - Age of animal. Codebook - Name of EEL codebook. ColorDict - Cell cluster color dictionary. Cycles - Number of barcoding cycles.<br> Expansion - Pixels the nuceli were expanded (pixelsize = 0.27um).<br> Expansion_um - Expansion of nuclei in micrometer.<br> Experiment - Experiment ID.<br> ExperimentDate - Date of experiment.<br> FOVoverlapPercentage - Overlap between field of view.<br> GenerationDate - Loom file generation date.<br> LOOM_SPEC_VERSION - Loompy version.<br> MaxHammingDist - maximum allowed Hamming distance.<br> Operator - Experiment operator.<br> Orientation - Cutting orientation.<br> Probes - Probe sequences file.<br> Protocol - Protocol used.<br> Quality - Manual evaluation of quality.<br> RNAfile - RNA file used<br> Removal - Method of removal of overlapping RNA in overlapping fields of view.<br> Sample - Sample ID<br> Segmentation - Segmentation algorithm.<br> Species - Species of sample.<br> Stitching - Field of view stitching method.<br> StitchingChannel - Between cycle alignment channel.<br> Strain - Strain of animal.<br> System - Microscope system used.<br> Tissue - Tissue in experiment.<br> TotalMolecules - Total number of molecules assigned to cells. <br> <strong>Column metadata</strong> X - X coordinate in pixels of 0.27um (multiply by 0.27 to get micrometer). X_um - X coordinate in micrometer. Y - Y coordinate in pixels of 0.27um (multiply by 0.27 to get micrometer). Y_um - Y coordinate in micrometer. tSNE_X - tSNE component 1. tSNE_Y - tSNE component 2. Clusters - Cluster label of each cell. TotalMolecules - Total molecules per cell. Cluster colors are saved as individual RGB values: R - Red. G - Green. B - Blue. (In the AnnData file, the tSNE and RGB values are availabe as a single array under "obsm" with keys "tSNE" and "RGB" respectively. ) <br> <strong>Row metadata</strong> Gene - Gene name. GeneTotal - Total number of detected molecules per gene.