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.
• "matrix of sampled 20k cells" contains the filtered gene-cell-barcode matrix of a randomly sampled 20k cells.
• 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.