|
| Status |
Public on Apr 26, 2023 |
| Title |
Col-0 root tips Col_control_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Col-0 root tips
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root tips
strain/line: Col-0
treatment: control
|
| Treatment protocol |
Seven days after sowing, the nylon mesh was transferred to either control 1/2 MS medium (control samples) or to 1/2 MS medium containing 0.5 ug/ml Bleomycin (bleomycin samples).
|
| Growth protocol |
For each sample, approximately 100 Col-0 seeds or 100 scl5 scl21 pat1 seeds were sown on top of a nylon mesh on squared plates holding 1/2 MS medium and 1% agar.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
0.2cm root tips were isolated and frozen in liquid nitrogen. RNA was extracted using QIAGEN Rneasy Plant Mini kit.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext® UltraTM RNALibrary Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Col_control_R1
|
| Data processing |
Illumina CASAVA software used for basecalling.
Paired-end reads were trimmed for adaptor sequences and aligned to the Araport11 exome using Salmon v0.9.1.
Transcript quantification was also performed by Salmon v0.9.1.
Assembly: Araport11 exome
Supplementary files format and content: tab-delimited text files generated from Salmon quantification, contain length of transcript in nucleotides, computed effective length, transcripts per million (TPM) and number of reads.
|
| |
|
| Submission date |
Apr 08, 2022 |
| Last update date |
Apr 26, 2023 |
| Contact name |
Bert De Rybel |
| E-mail(s) |
beryb@psb.vib-ugent.be
|
| Organization name |
VIB
|
| Department |
Center for Plant Systems Biology
|
| Lab |
Vascular Development
|
| Street address |
Technologiepark 71
|
| City |
Ghent |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE200500 |
PAT1-type GRAS-domain proteins control regeneration following wounding by transcriptional activation of DOF3.4 driving cell proliferation |
|
| Relations |
| BioSample |
SAMN27480256 |
| SRA |
SRX14787755 |
