|
| Status |
Public on Jul 02, 2020 |
| Title |
Arabidopsis root cells - sc_53 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis root cells
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/background: Col-0
genotype: shr-2
tissue: Root
use for atlas: No
|
| Growth protocol |
Seeds from wildtype Arabidopsis thaliana ecotype Columbia (Col-0), shortroot-2 (Col-0 background), and scarecrow-4 (Landsberg background backcrossed to Col-0 at least 5 times) were surface sterilized with a 50% (v/v) bleach, 0.05% (v/v) Tween-20 solution for 10 minutes and subsequently stratified for 48 hours at 4°C. Seeds were sown at a density of ~150-300 seeds/row on 1X Linsmaier and Skoog (LSP03-1LT, Caisson Labs; pH 5.7), 1% sucrose media covered by 100/ 47 µm mesh. Plates were placed vertically in a Percival chamber programmed to 16h light, 8h dark conditions at 22°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chromium Single Cell 3ʹ GEM Kit v3.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Arabidopsis root cells - Benfey Lab
Single-cell RNA-seq
|
| Data processing |
Processed by COPILOT (https://github.com/Hsu-Che-Wei/COPILOT).
Genome_build: TAIR10
Supplementary_files_format_and_content: *_mtx.tar: Include gene-by-cell count matrices.
Supplementary_files_format_and_content: *_COPILOT.rds: Seurat objects.
|
| |
|
| Submission date |
Jun 18, 2020 |
| Last update date |
Jul 02, 2020 |
| 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 |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE152766 |
Single-cell RNA-seq data of Arabidopsis root |
|
| Relations |
| BioSample |
SAMN15315808 |
| SRA |
SRX8574743 |
