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Sample GSM4809926 Query DataSets for GSM4809926
Status Public on Jan 01, 2021
Title 00 hour rep 2
Sample type SRA
Source name root tissue
Organism Arabidopsis thaliana
Characteristics tissue: root tissue
experiment: 00 hour
strain: Col-0
Treatment protocol Seeds were placed on 0.5 LS+0.8% bacto-agar plate following a specific pattern to avoid seedling collision during the lateral root bend essay.  The plate was stratified during 120 hours, grown vertically for 96 hours at 22°C, rotated 90°C while keeping vertically and grown for an additional 20 hours.
Growth protocol For all plant experiments, Arabidopsis seeds were sown on 0.5× LS 0.8% agar plates, stratified at 4°C for 2 days, and grown in continuous light conditions at 22°C for respective experimental design.
Extracted molecule total RNA
Extraction protocol Protoplast isolation was done according to Bargmann and Birnbaum (2010), with slight modifications.
10X genomics protocol
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description single cell RNA-seq data from 08 hour experiment
Data processing Illumina Nextseq 500 base caller is used
cellranger mkfastq was run on the nextseq output to generate fastq files
cellranger counts was run on output fastq files from each sample, to identify barcodes with sufficient reads for analysis, and to align reads to the Arabdiopsis genome using the Araport annotation.
cellranger aggr was then used to combine samples into one matrix and barcode set
Genome_build: TAIR10/ARAPORT
Supplementary_files_format_and_content: matrix.mtx is the UMI count matrix for the number of UMIs, each barcode (cell) had associated with each gene; barcodes.tsv contains barcode info, as well as experiment of origin and cell type label; genes.tsv
Submission date Sep 29, 2020
Last update date Jan 01, 2021
Contact name Christine Queitsch
Phone 206-685-8935
Organization name University of Washington
Department Genome Sciences
Lab Queitsch Lab
Street address 3720 15th Ave NE, Foege Hall
City Seattle
State/province WA
ZIP/Postal code 98105
Country USA
Platform ID GPL19580
Series (1)
GSE158761 A single cell view of the transcriptome during lateral root initiation
BioSample SAMN16293294
SRA SRX9215962

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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