smdavisjr / hasel_et_al

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.

Code

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

Code included in repository:

No custom code included in analysis pipelines.

Data

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

Acknowledgements

Data analysis was completed by Philip Hasel and Jessica Sadick.