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Sample GSM4626007 Query DataSets for GSM4626007
Status Public on Jul 02, 2020
Title Arabidopsis root cells - sc_52
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 SAMN15315809
SRA SRX8574742

Supplementary file Size Download File type/resource
GSM4626007_sc_52_COPILOT.rds.gz 3.0 Gb (ftp)(http) RDS
GSM4626007_sc_52_mtx.tar.gz 85.2 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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