|
| Status |
Public on Jul 02, 2020 |
| Title |
Single-cell RNA-seq data of Arabidopsis root |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
We report both raw and processed scRNA-seq data that are used to build transcriptomic atlas of Arabidopsis root.
|
| |
|
| Overall design |
scRNA-seq of 18 wild-type, 2 scr-4 and 2 shr-2 mutant Arabidopsis root samples. Three wild-type samples are from published data (two from Denyer et al. 2019 [PMID: 30913408] and one from Ryu et al. 2019 [PMID: 30718350]).
Denyer et al. (GSE123818): GSM3511858, WT Arabidopsis root cells - dc1; GSM3511859, WT Arabidopsis root cells - dc2
Ryu et al. (GSE123013): GSM3490689, WT Arabidopsis root cells - pp1
|
| |
|
| Contributor(s) |
Shahan R, Hsu C, Nolan T, Cole BJ, Taylor IW, Greenstreet L, Zhang S, Afanassiev A, Vlot A, Schiebinger G, Benfey PN, Ohler U |
| Citation(s) |
35134336, 36181683 |
| |
| Submission date |
Jun 18, 2020 |
| Last update date |
Oct 27, 2022 |
| Contact name |
Philip N. Benfey |
| Organization name |
Duke University
|
| Department |
Biology
|
| Lab |
Benfey Lab
|
| Street address |
130 Science Drive
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
|
| Samples (19)
|
|
| Relations |
| Reanalysis of |
GSM3490689 |
| Reanalysis of |
GSM3511858 |
| Reanalysis of |
GSM3511859 |
| BioProject |
PRJNA640389 |
| SRA |
SRP267870 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE152766_Columella_Atlas.rds.gz |
3.7 Gb |
(ftp)(http) |
RDS |
| GSE152766_Epidermis_LRC_Atlas.rds.gz |
19.6 Gb |
(ftp)(http) |
RDS |
| GSE152766_Ground_Tissue_Atlas.rds.gz |
10.0 Gb |
(ftp)(http) |
RDS |
| GSE152766_RAW.tar |
73.0 Gb |
(http)(custom) |
TAR (of RDS, TAR) |
| GSE152766_Root_Atlas.rds.gz |
44.6 Gb |
(ftp)(http) |
RDS |
| GSE152766_Root_Atlas_seu4.rds.gz |
44.8 Gb |
(ftp)(http) |
RDS |
| GSE152766_Root_Atlas_spliced_unspliced_raw_counts.rds.gz |
2.0 Gb |
(ftp)(http) |
RDS |
| GSE152766_Stele_Atlas.rds.gz |
15.5 Gb |
(ftp)(http) |
RDS |
| GSE152766_col0_COPILOT.rds.gz |
3.2 Gb |
(ftp)(http) |
RDS |
| GSE152766_dc1_COPILOT.rds.gz |
1.7 Gb |
(ftp)(http) |
RDS |
| GSE152766_dc2_COPILOT.rds.gz |
1.6 Gb |
(ftp)(http) |
RDS |
| GSE152766_pp1_COPILOT.rds.gz |
3.9 Gb |
(ftp)(http) |
RDS |
| GSE152766_rc.integrated_scr.rds.gz |
6.2 Gb |
(ftp)(http) |
RDS |
| GSE152766_rc.integrated_shr.rds.gz |
6.4 Gb |
(ftp)(http) |
RDS |
| GSE152766_rc.integrated_wt_shr_scr.rds.gz |
36.2 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_10_at_COPILOT.rds.gz |
4.5 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_11_COPILOT.rds.gz |
4.5 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_12_COPILOT.rds.gz |
5.6 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_1_COPILOT.rds.gz |
4.4 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_20_COPILOT.rds.gz |
6.0 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_21_COPILOT.rds.gz |
4.7 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_25_COPILOT.rds.gz |
3.9 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_30_COPILOT.rds.gz |
4.8 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_31_COPILOT.rds.gz |
4.1 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_36_COPILOT.rds.gz |
2.9 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_37_COPILOT.rds.gz |
2.8 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_40_COPILOT.rds.gz |
3.5 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_51_COPILOT.rds.gz |
3.1 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_52_COPILOT.rds.gz |
3.0 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_53_COPILOT.rds.gz |
4.0 Gb |
(ftp)(http) |
RDS |
| GSE152766_sc_9_at_COPILOT.rds.gz |
1.9 Gb |
(ftp)(http) |
RDS |
| GSE152766_tnw1_COPILOT.rds.gz |
2.4 Gb |
(ftp)(http) |
RDS |
| GSE152766_tnw2_COPILOT.rds.gz |
2.0 Gb |
(ftp)(http) |
RDS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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