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.