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Sample GSM2042527 Query DataSets for GSM2042527
Status Public on Jul 28, 2016
Title cat2 0h photorespiratory stress rep1
Sample type SRA
 
Source name cat2 0h photorespiratory stress
Organism Arabidopsis thaliana
Characteristics developmental stage: seedling
age: 3-week-old
tissue: shoot
ecotype: Columbia-0
genotype/variation: cat2
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 cat-0H-I_S4
Control sample cat2
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 SAMN04430377
SRA SRX1538071

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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