|
| Status |
Public on Jan 25, 2018 |
| Title |
Col-0 DMSO_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype: wild type
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 |
| |
|
| Description |
Sample same as GSM2918403
|
| 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 |
| Reanalysis of |
GSM2918403 |
| BioSample |
SAMN08391659 |
| SRA |
SRX3598174 |
