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Sample GSM2045526 Query DataSets for GSM2045526
Status Public on Jun 10, 2016
Title cat2-2 High light rep1
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
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 cat2-2 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 High light
c-3h-I_S4.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 6 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)
GSE77171 Photorespiratory stress in catalase deficient plants
Relations
BioSample SAMN04437605
SRA SRX1543235

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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