|
| Status |
Public on Dec 02, 2024 |
| Title |
Set2, Col-0, ctrl, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
10-day-old whole seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 10-day-old whole seedling
genotype: Col-0
treatment: control
|
| Treatment protocol |
Seedlings were either untreated or treated for the indicated hours with gaseous MeJA
|
| Growth protocol |
Arabidopsis seedlings were grown for 10 days under long day conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of Col-0 seedlings was extracted using RNeasy Plant Mini Kit (Qiagen).
cDNA library preparation was carried out with a TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq reads were aligned to the TAIR10 genome using STAR software (version 2.7.5a).
Transcripts were quantified for each sample with RSEM (version 1.3.3).
Differentially expressed genes between ctrl and 2h JA samples in each of the two sets (Set1: two biologcal repliactes, Set2: three biological replicates) were identified with edgeR (version 3.36.0).
Assembly: TAIR10
Supplementary files format and content: genes.results files including TPM and FPKM values for each sample.
Supplementary files format and content: edgeR analysis output as tab-delimited text files
|
| |
|
| Submission date |
Dec 08, 2023 |
| Last update date |
Dec 02, 2024 |
| Contact name |
Mark Zander |
| E-mail(s) |
[email protected]
|
| Organization name |
Rutgers State University of New Jersey
|
| Street address |
190 Frelinghuysen Rd
|
| City |
Piscataway |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE249737 |
High-throughput capture of transcription factor-driven chromatin dynamics using PHILO ChIP-seq (RNA-Seq) |
| GSE249738 |
High-throughput capture of transcription factor-driven chromatin dynamics using PHILO ChIP-seq |
|
| Relations |
| BioSample |
SAMN38735782 |
| SRA |
SRX22836392 |
