|
| Status |
Public on Dec 15, 2021 |
| Title |
WT_10_R1 |
| Sample type |
SRA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedlings
background ecotype: Col-0
genotype: WT1
age: 14 day-old
timepoint: 10
mutation type: wild type
batch: batch 1
|
| Treatment protocol |
flg22 peptide dissolved in DMSO (1 mg/mL) was added to the liquid MS for a final concentration of 3.3 uM. Treatment was conducted for three timepoints: 10 (not all samples), 30 and 60 minutes.
|
| Growth protocol |
Following 12 days of growth in MS 1% under sterile conditions at room temperature and long-days luminosity, seedlings were transferred to liquid MS media 1% and allowed to acclimate 48 hours at 130 rpm prior to treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A pool of 10 intact whole seedlings was flash frozen and total RNA was extracted using TRI-Reagent. Polysaccharide precipitation was carried out using the double sodium acetate method.
made by Novogene; Paired-end 150bp unstranded
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalling with Illumina Cassava 1.8
Cutadapt v1.18+52 was used to remove the adapters
Clean reads were mapped on the TAIR10 referennce genome using HISAT2, keeping only concordant paired alignments
SAM alignment files were converted into BAM, then wig and finally bigWig with normalization in CPM (counts per millions)
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files (unstranded data), normalized into CPM (counts per millions)
|
| |
|
| Submission date |
Jan 28, 2020 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Axel Thieffry |
| E-mail(s) |
axel.thieffry@gmail.com
|
| Organization name |
BioPhero-FMC
|
| Department |
R&D
|
| Street address |
Lersø Parkallé 42-44
|
| City |
Copenhagen |
| State/province |
Hovedstaden |
| ZIP/Postal code |
2100 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE144356 |
PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave |
|
| Relations |
| BioSample |
SAMN13932797 |
| SRA |
SRX7639793 |
