Code for the BRAIN Initiative Cell Census Network (BICCN) - RF1 Tilgner
Until recently, technological limitations prevented a genome-wide appraisal of the influence of isoform expression on the establishment and persistence of cell identity in various parts of the brain. Using an enhanced method of long-read single-cell isoform sequencing (ScISOr-Seq2), we performed a comprehensive analysis of RNA isoforms in mouse brain across multiple brain regions, cell subtypes, and a range of developmental timepoints from postnatal day 14 (P14) to adult (P56).
A detailed summary of the samples processed and links to raw data can be found on the BICCN portal. Nonetheless we are providing alist of samples and the data types available for each below:
| Age | Sex | Region | Replicates | 10x scRNA-Seq | PacBio | Oxford Nanopore |
|---|---|---|---|---|---|---|
| P14 | M | Hippocampus | 2 | ✔️ | ✔️ | ✔️ |
| P21 | M | Hippocampus | 2 | ✔️ | x | ✔️ |
| P28 | M | Hippocampus | 2 | ✔️ | ✔️ | ✔️ |
| P56 | M | Hippocampus | 2 | ✔️ | ✔️ | ✔️ |
| P14 | M | VisCortex | 2 | ✔️ | ✔️ | ✔️ |
| P21 | M | VisCortex | 2 | ✔️ | x | ✔️ |
| P28 | M | VisCortex | 2 | ✔️ | ✔️ | ✔️ |
| P56 | M | VisCortex | 2 | ✔️ | x | ✔️ |
| P56 | M | Striatum | 2 | ✔️ | ✔️ | ✔️ |
| P56 | M | Thalamus | 2 | ✔️ | ✔️ | ✔️ |
| P56 | M | Cerebellum | 2 | ✔️ | ✔️ | ✔️ |
An article describing this data and our findings can be found here
Custom code code used for processing and summarizing this data, files needed for this processing, and code used to generate plots for the manuscript is provided in this repo.
Additionally, the following raw and processed data is /will be made available on NeMO Links to mouse data:
- Short read Illumina reads fastqs
- Cellranger output files mtx, tsv,
- Raw long-read sequencing data sequenced on PacBio and ONT
- AllInfo files per processed ONT long read containing
- cell barcode
- assigned cell type
- UMI
- intron chain
- TSS assignment
- PolyA site assignment
- exon chain
- BED12 files per processed ONT long read
We additionally have data from 6 human hippocampal samples available through the NeMO
If you have questions, please do not hesitate to open an issue or reach out over email to me or the corresponding author.