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| Status |
Public on May 30, 2017 |
| Title |
lsd1-1 rep3 |
| Sample type |
SRA |
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| Source name |
lsd1-1_rosette
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| Organism |
Arabidopsis thaliana |
| Characteristics |
accession: Wassilewskija
genotype/variation: lsd1-1
age: 2-week-old
tissue: Rosette
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| 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.
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| 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.
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| 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 (www.nucleomics.be). Sequencing libraries were constructed with using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
lsd1-1
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| 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
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| Submission date |
Jun 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick Willems |
| E-mail(s) |
pawil@psb.ugent.be
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| Organization name |
Ghent University
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| Department |
PSB
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| Street address |
Technologiepark 927
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| City |
Gent |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE83262 |
Dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator in Arabidopsis |
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| Relations |
| BioSample |
SAMN05232031 |
| SRA |
SRX1838193 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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