TitleLaser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling
Data descriptionSingle-cell RNA-seq of human motor neurons rom post-mortem CNS tissues
Web-link of the paperhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941116
Data typescRNA-seq
Accession numberGSE76514
URL of the datahttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76514
TissuePost-mortem CNS tissues
Cell typeSpinal MNs
Number of cellsNA
Cell capture platformLCM-seq
Library preparation protocolSMART-seq2
Unique molecular identifier (Y/N)Y
Spike-in (Y/N)Y
Full-length (Y/N)Y
Brief summary of the scientific questionThey developed LCM-seq, an efficient and robust method that combines LCM and Smart-seq2. They apply LCM-seq on neurons isolated from mouse tissues, human post-mortem tissues, and illustrate its utility down to single captured cells and provide biological insight on highly similar neuronal populations
Brief summary of the bioinformatics processingGene expression analysis to identify MN marker genes;
Use Spearman’s correlation to compare gene expression among bulk, to demonstrate its utility to single cells;
PCA clustering to identify MN groups
CitationNichterwitz, S., Chen, G., Aguila Benitez, J., Yilmaz, M., Storvall, H., Cao, M., . . . Hedlund, E. (2016). Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling. Nat Commun, 7, 12139. doi:10.1038/ncomms12139
Web-link of the paperhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941116