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| Status |
Public on Dec 30, 2014 |
| Title |
RNA-Seq of single cells from the Arabidopsis root |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The definition of cell identity is a central problem in biology. Single-cell RNA-seq provides a wealth of information regarding the developmental state of individual cells. However, better methods are needed to map the identity of single cells, especially during identity transitions. We have developed a quantitative classification method that is robust to expression noise and can detect primary and chimeric identities from single-cell RNA sequencing profiles. The method uses existing transcriptome repositories of grouped cell-types to define a set of optimal cell-identity markers, which are then used to define a cell identity metric. This metric accurately classified diverse cell identities in Arabidopsis root tips and human glioblastoma cells. We demonstrate the strength of the approach to resolve a dynamic developmental process by analyzing the identity of single cells captured from regenerating Arabidopsis roots following removal of their stem-cell-niche. We discover that, apart from new niche formation at the vicinity of the cut site, cells that are distant from the injury site also undergo a transient, partial collapse of identity during the regeneration and reorganization of the root, demonstrating the usefulness of a quantitative cell identity metric.
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| Overall design |
4 Technical replicates (pooled-and-split single QC cells), 23 cells from the QC, 3 cells from the Stele, and 4 cells from the stele, 16h following root tip decapitation
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| Contributor(s) |
Efroni I, Ip P, Nawy T, Mello A, Birnbaum KD |
| Citation(s) |
25608970 |
| Submission date |
Apr 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Idan Efroni |
| E-mail(s) |
idan.efroni@mail.huji.ac.il
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| Organization name |
Hebrew University
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| Department |
Plant Sciences
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| Street address |
POB 12
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| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (31)
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| Relations |
| BioProject |
PRJNA198192 |
| SRA |
SRP021196 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE46226_SC_Expression.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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