Nuclei were isolated from ~25mg of fresh frozen C57/Bl6 adult mouse brain purchased from BioIVT following the Chromium Nuclei Isolation Reagent Kits Sample Prep User Guide (CG000505).
Gene Expression libraries were prepared following the Chromium Single Cell 3'v3.1 Reagent Kits User Guide (v3.1 Chemistry Dual Index, CG000315) and targeting 5,000 cells. Libraries were sequenced on an Illumina NovaSeq instrument targeting 20,000 reads per cell.
Sequencing data was processed using Cell Ranger, with web summary and output files available below.
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Sequencing instrument: Illumina NovaSeq 6000
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Sequencing depth: 27,734 mean reads per cell
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Sequencing configuration: Paired-end, dual indexing
- Read 1: 28 cycles (16 bp barcode, 12 bp UMI)
- i5 index: 10 cycles (sample index)
- i7 index: 10 cycles (sample index)
- Read 2: 90 cycles (transcript)
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Cells detected: 7,377
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Median genes per cell: 2,168
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Median UMIs per cell: 4,319
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| Input Files | Size | md5sum |
|---|---|---|
| FASTQs | 19.8 GB | 9cf158647d883ffdf97cf21780d3deaa |
| Output Files Format details | Size | md5sum |
|---|---|---|
| Genome-aligned BAM | 14.4 GB | f2ae4faac03dc31d590fb4b0eded06d6 |
| Genome-aligned BAM index | 5.62 MB | b3bae960c14ef1c38421576a2da09f70 |
| Per-molecule read information | 321 MB | 17be4c1c196355c3b112fabba6e8cec9 |
| Feature / cell matrix HDF5 (filtered) | 23.1 MB | 60ed2ff52c09c383c65d5b2a70b2fa04 |
| Feature / cell matrix (filtered) | 60.5 MB | 843f669677edf0373acb2c0c7b481654 |
| Feature / cell matrix HDF5 (raw) | 69.5 MB | 6b6dfe30c9db03fdb62fa8f82bfedc89 |
| Feature / cell matrix (raw) | 163 MB | d22785d66f07002a959877918bfa035c |
| Clustering analysis | 36 MB | 100c6e8a906ae047cf774a06f21e53ed |
| Summary CSV | 652 B | 983d3f0bc8f4cadc86b6cc2ac6302938 |
| Summary HTML | 3.6 MB | 3ec12879d2cbee903e8630761fdfec83 |
| Loupe Browser file | 90.6 MB | a3329443f0d159091f2d7adf256c1d85 |