MCA DGE Data

MCA single cell DGE data (Cells with &gt;500UMI ) for the following manuscript:Mapping the Mouse Cell Atlas by Microwell-seq<br>MCA_DGE.rar: The raw digital expression matrix (dge) of more than 400,000 single cells sorted by tissues. For each cell, more than 500 transcripts are expressed. The batch effects are not been removed.<br>MCA_Figure2-batch-removed.txt.tar.gz: The batch removed dge of approximately 60,000 cells of high quality. 1500 cells were sampled from 43 tissues respectively. This sampled data is used for Figure 2.<br>MCA_cell-assignments.xlsx: The annotation of cells, which includes the cell names, cluster ID, belonged tissues, experimental batches and cell barcodes.<br>MCA_All-batch-removed.zip: The batch effect removed dge of more than 400,000 single cells sorted by tissues. This dataset can be used to make global tissue tSNE plot and do cross-tissue analysis.<br>Batch effect removalFor cross tissue comparison, we removed the batch gene background to improve presentation. We assume that for each batch of experiment, the cell barcodes with less than 500UMI correspond to the empty beads exposed free RNA during the cell lysis, RNA capture and washing steps. The batch gene background value is defined as the average gene detection for all cellular barcodes with less than 500 UMI, multiplied by a coefficient of 2, and then rounded to the nearest integer. Genes detected in less 25% of all cells are removed from the batch gene background list. We subtract the batch gene background for each cell from the digital expression matrix before making the cross tissue comparison figures.