Hasel_et_al. 2021, Nature Neuroscience (https://www.nature.com/articles/s41593-021-00905-6)
ALL the mouse astrocytes!
Libraries (including version) used to analyze single cell RNASeq (scRNAseq) astrocyte data included in: Hasel et al. 2021, Nature Neuroscience.
Included is the github libraries and code necessary to replicate the Seurat objects used for analysis. The following versions of individual software/packages were used for analysis:
- R 3.6.2
- scds 1.1.2
- scater v1.13.23
- SpaceRanger v1.2.0
- edgeR v3.27.13
- Cell Ranger v3.0.2
- CATALYST 1.9.8
- UpSetR 1.4.0
- ComplexHeatmap v2.1.0
- ggplot2 v3.2.1
- dplyr v0.8.3
- purrr v0.3.3
- RColorBrewer v1.1-2
- viridis v0.5.1
- scran v1.13.25
- Seurat v3.1.0
- SingleCellExperiment v1.7.11
- muscat v0.99.9
- circlize v0.4.8
- VennDiagram v1.6.20
- HISAT2 v.2.1.0
- StringTie v2.1.1
- DESeq2 v2.11.40.6
- Prism8 v8.2.1
- LSD v4.0-0
No custom code included in analysis pipelines.
The original data analyzed in this project can be directly downloaded from the following source: XXX
Reanalysis of Astrocytes from Published Mouse Datasets: Primary sources for reanalyzed data is summarized below.
| Dataset | Seq Used | Data Repository | Publication |
|---|---|---|---|
| Habib | Chromium Single Cell 3' Gene Expression (v2, v3) | GSE143758 | Habib et al. (2020) Nature Neuroscience 23:701-706 |
| Wheeler | Drop-seq | GSE130119 | Wheeler et al. (2020) Nature 578:593-599 |
| Zamboni | Chromium Single Cell 3' Gene Expression (v2) | GSE139842 | Zamboni et al. (2020) Cell Stem Cell 27:605-617 |
| Zhou | Chromium Single Cell 3' and 5' Gene Expression | GSE140511 | Zhou et al. (2020) Nature Medicine 26:131-142 |
Data analysis was completed by Philip Hasel and Jessica Sadick.