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Sample GSM2197801 Query DataSets for GSM2197801
Status Public on May 30, 2017
Title lsd1-1 rep3
Sample type SRA
Source name lsd1-1_rosette
Organism Arabidopsis thaliana
Characteristics accession: Wassilewskija
genotype/variation: lsd1-1
age: 2-week-old
tissue: Rosette
Treatment protocol Dexamethasone (DEX) induction was performed for 35Spro:LSD1-GR line. 2-week-old seedlings grown on 20 micron nylon mesh (ELKO Filtering Co., Miami, FL, US) on MS medium were transferred to MS medium supplemented with 30 μM DEX (Sigma-Aldrich, Saint Louis, MO, US). Other lines did not undergo any treatment prior to total RNA isolation.
Growth protocol 2-week-old Ws-0, lsd1-1 mutant, 35Spro:LSD1-GFP and DEX-treated 35Spro:LSD1-GR plants grown on MS medium in 16 h photoperiod, PPFD: 100±25 µmol m ¯² s¯¹, temperature 22/18 °C day/night.
Extracted molecule total RNA
Extraction protocol Total RNA isolation was performed using GeneMATRIX Universal RNA Purification Kit (EURX, Gdansk, Poland) with additional step of on-column DNAse I treatment in three biological repeats.
Library preparation and sequencing was performed at the VIB Nucleomics Core ( 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 lsd1-1
Data processing Low quality base pairs (LEADING/TRAILING:10 and SLIDINGWINDOW:4:30) and short read sequences (min. length 36) were trimmed using Trimmomatic (v0.30).
Quality-filtered reads were aligned to the TAIR10 Arabidopsis reference genome using the spliced aligner GSNAP (version 2013-02-05)
The number of reads per gene was quantified using Htseq-count (v.0.6.1)
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Table containing gene counts for all 12 samples as delivered by Htseq-count
Submission date Jun 13, 2016
Last update date May 15, 2019
Contact name Patrick Willems
Organization name Ghent University
Department PSB
Street address Technologiepark 927
City Gent
ZIP/Postal code 9052
Country Belgium
Platform ID GPL19580
Series (1)
GSE83262 Dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator in Arabidopsis
BioSample SAMN05232031
SRA SRX1838193

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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