|
| Status |
Public on Jul 28, 2016 |
| Title |
Col-0 0h photorespiratory stress rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Col-0 0h photorespiratory stress
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: seedling
age: 3-week-old
tissue: shoot
ecotype: Columbia-0
genotype/variation: wt
stress: control
|
| Treatment protocol |
After 21 days of growth, the MicroporeTM surgical tape (3M) that sealed the plates was replaced by two layers of Parafilm M (Bemis) to restrict gas exchange. Plants were transferred to a continuous light regime.
|
| Growth protocol |
Plants were grown in Petri dishes (150×25 mm; Becton-Dickinson) on full-strength MS agar-solidified medium supplemented with 1% (w/v) sucrose, 100 mg/L myo-inositol, 0.5 mg L‑1 nicotinic acid, 0.5 mg/L pyridoxine, and 1 mg/L thiamine at 21°C and LD conditions (16 h light [100 μmol m−2 s−1]/8 h dark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a combination of TRIzol and RNeasy Kit (Qiagen) according to the manufacturers’ instructions.
Library preparation and sequencing was performed at the VIB Nucleomics Core (www.nucleomics.be). Sequencing libraries were constructed with using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Col-0H-III_S3
Control sample Col-0
Three-week-old seedlings (shoot tissue)
|
| Data processing |
Adapter sequences and low quality base-pairs (Q < 20) were trimmed using Trim Galore (v0.3.3, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), retaining high-quality reads of at least 50 bp length.
Quality-filtered reads were aligned to the TAIR10 Arabidopsis reference genome using the spliced aligner TopHat2 (v2.1.0)
The number of reads per gene was quantified using featureCounts function as implemented in the Subread package v1.4.6
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Table containing gene counts for all 24 samples as delivered by featureCounts
|
| |
|
| Submission date |
Jan 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick Willems |
| E-mail(s) |
pawil@psb.ugent.be
|
| Organization name |
Ghent University
|
| Department |
PSB
|
| Street address |
Technologiepark 927
|
| City |
Gent |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE77017 |
SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions |
|
| Relations |
| BioSample |
SAMN04430376 |
| SRA |
SRX1538070 |
