EEL Mouse 440 genes single cell data
Cell by gene matrix of the EEL mouse 440 gene experiment.
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.
Metadata
Age - Age of animal.
Codebook - Name of EEL codebook.
ColorDict - Cell cluster color dictionary.
Cycles - Number of barcoding cycles.
Expansion - Pixels the nuceli were expanded (pixelsize = 0.27um).
Expansion_um - Expansion of nuclei in micrometer.
Experiment - Experiment ID.
ExperimentDate - Date of experiment.
FOVoverlapPercentage - Overlap between field of view.
GenerationDate - Loom file generation date.
LOOM_SPEC_VERSION - Loompy version.
MaxHammingDist - maximum allowed Hamming distance.
Operator - Experiment operator.
Orientation - Cutting orientation.
Probes - Probe sequences file.
Protocol - Protocol used.
Quality - Manual evaluation of quality.
RNAfile - RNA file used
Removal - Method of removal of overlapping RNA in overlapping fields of view.
Sample - Sample ID
Segmentation - Segmentation algorithm.
Species - Species of sample.
Stitching - Field of view stitching method.
StitchingChannel - Between cycle alignment channel.
Strain - Strain of animal.
System - Microscope system used.
Tissue - Tissue in experiment.
TotalMolecules - Total number of molecules assigned to cells.
Column metadata
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. )
Row metadata
Gene - Gene name.
GeneTotal - Total number of detected molecules per gene.
