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Sample GSM2947242 Query DataSets for GSM2947242
Status Public on Jan 25, 2018
Title nia1/2 DMSO_rep1
Sample type SRA
 
Source name seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype: nia1/2
developmental stage: 6 days old seedlings
treatment: DMSO
tissue: seedlings
Treatment protocol Seedlings from a single flask were divided into to two new flasks with fresh growth medium. One of the flasks contained 600 nM isoxaben added from a 1000x stock dissolved in DMSO. The other flask contained equal amount of DMSO without isoxaben. Treatment was started at 9 am and the samples were collected at 10 am.
Growth protocol 30 mg of seeds were sterilized by sequential incubation with 70 % ethanol and 50 % bleach on a rotating mixer for 10 min each and washed 3 times with sterile water. Seeds were then transferred into 250 ml erlenmayer flasks containing 125 ml half-strength Murashige and Skoog growth medium (2.1 g/L Murashige and Skoog Basal Medium, 0.5 g/L MES salt and 1 % sucrose at pH 5.7). Seedlings were grown in long-day conditions (16 h light, 22°C / 8 h dark, 18°C) at 150 μmol m-2 s-1 photon flux density on a IKA KS501 flask shaker at a constant speed of 130 rotations per minute. Seedlings were grown for 6 days prior to treatment.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using a Spectrum Plant Total RNA Kit (Sigma-Aldrich). RNA concentration was measured using a Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and integrity assessed using a Agilent RNA 6000 Pico Kit.
RNA Seq libraries were prepared using a TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer's instructions. 500 ng total RNA was used as starting material.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Base-calling was performed on the NS500 instrument by Illumina RTA v2.4.6. FASTQ files were generated using bcl2fastq2 Conversion Software v1.8.4
Each FASTQ file was subjected to quality control trough fastQC v11.1
The reads were aligned to the A. thaliana genome (Ensembl v82) with STAR v2.4.1 in two-pass mode
The reads that aligned uniquely to the genome were aggregated into gene counts with FeatureCounts v1.4.6 using the genome annotations defined in Ensembl v82
Genome_build: A. thaliana genome (Ensembl v82)
Supplementary_files_format_and_content: Tab-separated values files including AGI code, chromosomes, start, end, length and read count values for each sample
 
Submission date Jan 24, 2018
Last update date Jan 25, 2018
Contact name Thorsten Hamann
E-mail(s) thorsten.hamann@ntnu.no
Organization name NTNU
Department Department of Biology
Street address Høgskoleringen 5
City Trondheim
ZIP/Postal code 7491
Country Norway
 
Platform ID GPL19580
Series (1)
GSE109613 Transcriptome analysis of isoxaben-induced loss of cell wall integrity in Arabidopsis nia1/2 mutant
Relations
BioSample SAMN08391653
SRA SRX3598180

Supplementary file Size Download File type/resource
GSM2947242_nia1-2-DMSO1.tsv.gz 1.4 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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