Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Single-cell RNA-seq for pGL2 and QC cells from the Arabidopsis thaliana root

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jong Kyoung Kim

PROVIDER: E-MTAB-1499 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Accounting for technical noise in single-cell RNA-seq experiments.

Brennecke Philip P Anders Simon S Kim Jong Kyoung JK Kołodziejczyk Aleksandra A AA Zhang Xiuwei X Proserpio Valentina V Baying Bianka B Benes Vladimir V Teichmann Sarah A SA Marioni John C JC Heisler Marcus G MG

Nature methods 20130922 11

Single-cell RNA-seq can yield valuable insights about the variability within a population of seemingly homogeneous cells. We developed a quantitative statistical method to distinguish true biological variability from the high levels of technical noise in single-cell experiments. Our approach quantifies the statistical significance of observed cell-to-cell variability in expression strength on a gene-by-gene basis. We validate our approach using two independent data sets from Arabidopsis thaliana ...[more]

PMID: 24056876

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Dataset Information

Single-cell RNA-seq for pGL2 and QC cells from the Arabidopsis thaliana root

Publications

Accounting for technical noise in single-cell RNA-seq experiments.

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