E-MTAB-1499 - RNA-seq of coding RNA from pGL2 and QC cells from the Arabidopsis thaliana root to demonstrate our method of controlling for technical noise in single-cell RNA-seq experiment

Released on 21 March 2013, last updated on 14 March 2016
Arabidopsis thaliana
Samples (20)
Protocols (5)
To demonstrate our method of controlling for technical noise in single-cell RNA-seq experiments we manually collected single A. thaliana cells marked by the expression of green fluorescent protein (GFP) driven by either the GL2 or WOX5 promoters. Seven and six cells were collected from each cell type, respectively. The GL2 promoter marks the non-hair cells in the root epidermis whereas the WOX5 promoter specifies the quiescent center (QC) of the root. Each cell selected was processed together with 50 pg of total HeLa RNA spike-in to prepare RNA-seq libraries using the Tang protocol. For comparison, we again added the commercially available ERCC spike-ins. We also performed RNA-seq on a set of technical replicates of total A. thaliana RNA using starting amounts ranging from 5000pg down to 10pg, a range that covers the RNA content obtainable from single cells of various sizes.
Experiment types
RNA-seq of coding RNA, co-expression, in vivo
Accounting for technical noise in single-cell RNA-seq experiments. Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG. , Europe PMC 24056876
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-MTAB-1499.idf.txt
Sample and data relationshipE-MTAB-1499.sdrf.txt