|
| Status |
Public on Jun 10, 2016 |
| Title |
cat2-2 gox1 High CO2 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Three-week-old seedlings (shoot tissue)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaf
age: 3-week-old
ecotype: Columbia-0
genotype: cat2-2, gox1
|
| Treatment protocol |
For high light treatments, 3-week-old plants were transferred to a Sanyo Fitotron plant growth chamber in ambient air conditions (400 ppm CO2, relative humidity of 55%, 21°C) and irradiation of 1,200 umol m-1 s-1 for three hours. Middle aged leaves of 15 individual plants per line were sampled, pooled and frozen in liquid nitrogen. This entire set-up was repeated to obtain three biological repeats.
|
| Growth protocol |
cat2 gox1 and cat2 gox2 mutant plants were grown under elevated CO2 concentrations (3,000 ppm) to impair photorespiration. Individual plants were organized according to a completely randomized block design in a controlled climate chamber (Votsch Industrietechnik) in a 16:8 day/night regime (relative humidity of 75%, 21°C and an irradiance of 120 umol m-2 s-1).
|
| 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 |
cat2-2 gox1 High CO2
cg1-0h-II_S8.fastq.gz
|
| 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 12 samples as delivered by featureCounts
|
| |
|
| Submission date |
Jan 25, 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) |
| GSE77170 |
Arabidopsis GLYCOLATE OXIDASE 1 and 2 display divergent roles under conditions promoting photorespiration |
|
| Relations |
| BioSample |
SAMN04437609 |
| SRA |
SRX1543221 |
