All methods and relevant materials are discussed in detail in SI Appendix, SI Methods . The single cell analysis pipeline consisted of the following steps. Brain tissue was dissociated and single cell suspensions were loaded on a medium-sized C1 Single-Cell Auto Prep Array for mRNA Seq available (Fluidigm). cDNA was converted into sequencing libraries using a Nextera XT DNA Sample Preparation Kit (Illumina). Raw sequencing reads were aligned using STAR and per gene counts were calculated using HTSEQ. Gene counts were further analyzed using R. Patients were consented for the acquisition of specimens through a process approved by the Stanford Hospital Institutional Review Board.
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Single-Cell RNA Sequencing of Brain Tissue
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Corresponding Organization :
Other organizations : Stanford University, Institute of Neurobiology
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Variable analysis
independent variables
- Not explicitly mentioned
- Not explicitly mentioned
- Brain tissue dissociation and single cell suspensions
- Loading single cell suspensions on a medium-sized C1 Single-Cell Auto Prep Array for mRNA Seq
- CDNA conversion into sequencing libraries using a Nextera XT DNA Sample Preparation Kit (Illumina)
- Raw sequencing reads alignment using STAR and per gene counts calculation using HTSEQ
- Gene counts analysis using R
- Patient consent and approval by the Stanford Hospital Institutional Review Board
- Positive control: Not mentioned
- Negative control: Not mentioned
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