|
| Status |
Public on Sep 26, 2023 |
| Title |
S12_60mM.KNO3_2.5nM.isoxaben_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root
genotype: Col-0
treatment: 60mM.KNO3_2.5nM.isoxaben
|
| Treatment protocol |
Long term treatment: seedlings grown on KNO3-adjusted media containing 2.5 nM isoxaben or mock - roots harvested 6 days after stratification. Shift/short-term experiment: seedlings grown on polyester mesh on KNO3-adjusted media, then on day 5 shifted to media containing the same concentration of KNO3 with 2.5 nM isoxaben or mock - roots harvested at 6 days after stratification.
|
| Growth protocol |
Seedlings grown vertically on 1x MS media with 0.8% agar, modified to contain either 6 mM or 60 mM KNO3. Three days stratification, then moved to growth cabinet set to 21C/19C 16h/8h light/dark, under LED lighting at 100 uE.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frozen roots added to 2 mL tube with 5 mm zirconia ball. Frozen tissue ground with Retsch Mill. Qiagen Rneasy Plant Mini Kit used to extract RNA.
Libraries prepared using polyA enrichment by BGI (Hong-Kong) for DNBSEQ platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
12-60mMisx
S12
cts_str2_STARout_allsamples.txt
nCts_DESeq2_allsamples.txt
|
| Data processing |
data filtering (removing adapter sequence, contamination, and low-quality reads) with SOAPnuke (BGI); filter parameters："-n 0.03 -l 20 -q 0.4 -A 0.28"; delete the entire read if more than 28% match the adapter sequence; delete the entire read if there are more than 40% bases having a quality value lower than 20; delete the entire read if there are more than 3% N in the read
read alignment with STAR v2.7.9a
counts per gene normalized by median of ratios method with DESeq2 v1.32.0
Assembly: TAIR10 release 51
Supplementary files format and content: cts_str2_STARout_allsamples.txt : tab-delimited text file, STAR read counts per gene in each sample
Supplementary files format and content: nCts_DESeq2_allsamples.txt : tab-delimited text file, DESeq2 normalized read counts per gene in each sample
|
| |
|
| Submission date |
Apr 02, 2023 |
| Last update date |
Sep 26, 2023 |
| Contact name |
Sarah J Whitcomb |
| Organization name |
USDA-ARS
|
| Department |
Cereal Crops Research Unit
|
| Street address |
502 Walnut St
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53726 |
| Country |
USA |
| |
|
| Platform ID |
GPL28290 |
| Series (1) |
| GSE228764 |
Cellulose biosynthesis inhibitor isoxaben causes nutrient-dependent and tissue-specific Arabidopsis phenotypes |
|
| Relations |
| BioSample |
SAMN34042541 |
| SRA |
SRX19846009 |
