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| Status |
Public on Mar 19, 2024 |
| Title |
Arabisopsis root cells - sc_132 |
| Sample type |
SRA |
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| Source name |
Root
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Root
cell type: All cell types of root
genotype: pCVP2:BRI1-Citrine_bri1-T
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| Growth protocol |
Arabidopsis accession Columbia-0 (Col-0) was used as wild type. The following lines were previously described: bri1 GABI_134E10 (Jaillais et al., 2011); bri1-116brl1brl3 triple mutant (bri1-T) (Irani et al., 2012); pGL2:BRI1-GFP/bri1-T (Vragović et al., 2015); gtl1-1 (WiscDsLox413-416C9), df1-1 (SALK_106258), and gtl1-1 df1-1 (Shibata et al., 2018); JKD-Ypet recombineering line (Moreno-Risueno et al., 2015). Seeds were sterilized using 50% (v/v) bleach with 0.05% Tween-20 for 10-15 minutes, plated on 1/2 Linsmaier and Skoog (LSP03-1LT, Caisson Labs; pH 5.7), 1% sucrose media, and stratified 2-4 days at 4°C in the dark. Plates were kept vertically in a Percival growth chamber set to 22°C, 16 hours light/8 hours dark and grown for 7 days unless otherwise indicated. Chemical treatments were conducted by cooling the growth media to approximately 60°C after autoclaving and adding DMSO (a mock solvent), 1μM Brassinazole (BRZ, SML1406, Sigma) or 100nM Brassinolide (BL, 21594, Cayman Chemical).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Chromium Single Cell 3ʹ GEM Kit v3 and v3.1
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X Genomics kit v3.1
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| Data processing |
Processed by COPILOT (https://github.com/ohlerlab/COPILOT)
Assembly: TAIR10
Supplementary files format and content: Seurat object
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| Submission date |
Mar 15, 2024 |
| Last update date |
Mar 19, 2024 |
| 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 |
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| Platform ID |
GPL26208 |
| Series (1) |
| GSE212230 |
Single-cell RNA-seq of brassinosteroid response in Arabidopsis roots |
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| Relations |
| BioSample |
SAMN40472747 |
| SRA |
SRX23961715 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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