EEL mouse sagittal 440 genes spatial RNA data

Raw RNA locations of a sagittal mouse brain section produced by EEL FISH for 440 genes.

The file contains 11249762 rows and 7 columns.

The RNA file is in the .parquet file format which can be opened with FISHscale (https://github.com/linnarsson-lab/FISHscale) or any other parquet file reader (https://arrow.apache.org/docs/index.html).  

Alternatively, there is also a .csv file with the RNA data. However, it is more that 1GB and the .parquet file will be more efficient.

RNA .parquet or .csv files

Position and gene label for all RNA molecules.

"c_px_microscope_stitched" contains X coordinates.

"r_px_microscope_stitched" contians Y coordinates.

The unit are pixels with a size of 0.18 micrometer. Multiply by 0.18 to get um scale.

"c_transformed" contains X coordinates.

"r_transformed" contains Y coordinates.

The units are pixels with a size of 0.27 micrometer. Multiply by 0.27 to get um scale. These coordinates match the coordinates in the single cell .loom file.

"decoded_genes" contains the gene label for each point. Note that there are 8 empty barcodes as negatie controls, labeled "Control1" to "Control8". There is also a gene called  "Cre" that is not present in this sample. Please remove controls and Cre before analysing any biological questions.

"hamming_distance" is the hamming distance divided by the barcode length (16). The closer to 0 the better the barcode.

"Valid" Boolean colum where detected RNA molecules that are inside the tissue section are labeled with a 1.

Tissue polygon .csv file

The .csv flie contains a polygon of the tissue area to clip RNA molecules outside. This was used to generate the "Valid" column. The unit size is in micrometer.

Gene colors .pkl file

Pickled Python dictionary with gene colors used in the paper.