|
| 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
matrix.mtx
barcodes.tsv
genes.tsv
|
| 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 |
| E-mail(s) |
queitsch@uw.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN16293294 |
| SRA |
SRX9215962 |
