1.3 Million Brain Cells from E18 Mice

Cells from cortex, hippocampus and subventricular zone of two E18 mice

• Combined cortex, hippocampus, and subventricular zone were purchased from BrainBits (C57EHCV). They were from 2 E18 C57BL/6 mice dissected on the same day, shipped overnight on ice, and stored at 4C until being prepared for scRNA-Seq.
• Brain tissues were dissociated following the Demonstrated Protocol for Mouse Embryonic Neural Tissue.
• 69 scRNA-Seq libraries were made from first mouse brain 2 days after the dissection. Another 64 scRNA-Seq libraries were made from second mouse brain 6 days after the dissection.
• 26bp Read 1 (16bp Chromium barcode and 10bp UMI), 98bp Read 2 (transcript), and 8bp i7 sample barcode for each scRNA-Seq library
• Sequenced on 11 Illumina Hiseq 4000 flow cells, and each sample was sequenced on multiple flow cells. Samples were downsampled and aggregated with approximately 18,500 reads per cell.
• 1,306,127 cells detected in total
• "aggr - Gene/cell matrix HDF5 (filtered)" contains the filtered matrix in HDF5 format. To load and process the matrix, please see our guided Python tutorial. Note that the file is too large to be loaded in R.
• "matrix of sampled 20k cells" contains the filtered gene-cell-barcode matrix of a randomly sampled 20k cells. This file can be opened in R using the function get_matrix_from_h5 in the Cell Ranger: R Kit.
• Cell Ranger commands used to produce this aggregated dataset:

cellranger count --cells=10000 ...

cellranger aggr --id=neuron_aggregation --csv=aggregator.csv --nosecondary

cellranger reanalyze --id=neuron_reanalyze --matrix=filtered_matrix.h5 --params=reanalyze.csv

The instructions to download FASTQ files are here. The instructions to download BAM files from GEO are here.

This dataset is licensed under the Creative Commons Attribution license.