|
| Status |
Public on Mar 23, 2022 |
| Title |
TRAP_DMSO_2 |
| Sample type |
SRA |
| |
|
| Source name |
roots
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: transgenic line ubiquitously expressing a GFP-tagged RPL27
assay: TRAP
treatment: DMSO
tissue: roots
replicate: 2
|
| Treatment protocol |
At 7 DAG, samples were treated for 16h with either with 10 µM AZD8055 or DMSO control media before being transferred to DMSO, 10 µM IAA, 10 µM AZD8055 or 10 µM AZD8055 + 10 µM IAA.
|
| 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.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Root tissues were dissected after 6h. All sampling were performed in triplicate. For each sample, about 1500 segments of the lower two-thirds of the seedling roots were pooled, flash frozen in liquid nitrogen and later homogenised with a polysome-extraction buffer (Thellmann et al, 2020). The suspension was centrifuged for 15 min (16 000 g, 4°C). An aliquot of the homogenate was used for Bulk-RNA-extraction by use of TRIzol reagent (Invitrogen). The remaining supernatant was incubated with GFP-Trap® Magnetic Agarose beads (Chromotek, Munich, Germany). Ribosomal bound RNA was obtained by immunoprecipitation with magnetic anti-GFP beads in accordance with the manufacturer’s instructions and subsequently purified by use of TRIzol reagent (Invitrogen).
Illumina NextSeq libraries were prepared from 2 µg of total RNA (bulk) or 100ng (Ribosome bound) after depleting the rRNA via Ribo-Zero Plus rRNA Depletion Kit (Illumina) and sequencing performed on NextSeq 500 flow cells (12 samples per cell).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
total RNA - RiboZero
TRAP_01
|
| 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 23, 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) |
| GSE199203 |
Profiling of bulk and ribosome associated mRNA of Arabidopsis roots upon lateral root induction upon TOR activity inhibition with AZD8055 [dataset2] |
| GSE199211 |
TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN26886321 |
| SRA |
SRX14574421 |
