|
| Status |
Public on Mar 23, 2022 |
| Title |
UB10pro_amiR-TOR_NPA_2 |
| Sample type |
SRA |
| |
|
| Source name |
roots
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: UB10pro_amiR-TOR
treatment: NPA
replicate: 2
tissue: roots
|
| Treatment protocol |
Samples were then transfered either to 10 µM NPA and 10 µM Estradiol (NPA_Es) or DMSO control (NPA) for additional 24 h before being shifted to either 10 µM IAA + 10 µM Estradiol (IAA_Ees) or DMSO (IAA) for LR induction or maintained on the same plates. Root tissue was harvested after 6 h. All sampling points were performed in triplicate.then transferred to plates containing 10µM IAA, and 10µM DEX and DMSO control. Root tissue was harvested at 0, 2, 4 and 6 h after transfer onto auxin plates. All sampling points were performed in triplicate. For each sample, app. 200 segments of the lower two-thirds of the seedling roots were pooled.
|
| Growth protocol |
Seeds were germinated on Nitex membranes (Sefar) on 0.5X MS medium and transferred 7d after germination under 16h light/8h dark conditions to 10µM NPA for 24h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Root samples were flash frozen in liquid nitrogen, RNA was extracted with the Universal RNA purification kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped onto the Arabidopsis thaliana genome (TAIR10) and numbers of reads per transcripts computed using STAR (version 2.5.2b) with options: --runThreadN 36 --quantMode TranscriptomeSAM GeneCounts
Subsequent analysis of differentially expressed genes was performed in R using the DEseq2 package (Love, M. I. et al. Genome Biology 15, (2014))
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include counts values per transcript for each Sample
|
| |
|
| Submission date |
Mar 23, 2022 |
| Last update date |
Mar 24, 2022 |
| Contact name |
Alexis Maizel |
| E-mail(s) |
alexis.maizel@cos.uni-heidelberg.de
|
| Organization name |
Heidelberg University
|
| Department |
Center for Organismal Studies
|
| Street address |
Im Neuenheimer Feld 230
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE199202 |
Transcriptome profiling of Arabidopsis roots upon lateral root induction in WT and TOR knock down [dataset1] |
| GSE199211 |
TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN26886335 |
| SRA |
SRX14574457 |
