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| Status |
Public on Feb 22, 2019 |
| Title |
Root_Si_2 |
| Sample type |
SRA |
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| Source name |
Root_Si
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| Organism |
Brassica napus |
| Characteristics |
treatment: Si
genotype: wild type
date: planting date=21-03-17, harvest date=28-03-17
tissue: roots
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| Growth protocol |
In a greenhouse, seeds of Brassica napus L. var. “Citizzen” were germinated on perlite over deionized water for 4 days in the dark. Then seedlings were transferred to natural light conditions and supplied with nutrient solution for 10 days containing: NH4NO3 (1mM), K2SO4 (1mM), KH2P04 (0.4mM), K2HPO4 (0.15mM), CaCl2 (3mM), MgSO4 (0.5mM), EDTA-2NaFe (0.2mM), H3BO3 (14µM), MnSO4 (5µM), ZnSO4 (3µM), CuSO4 (0.7µM), (NH4)6Mo7O24 (0.7µM), CoCl2 (0.1µM), NiCl2 (1µM). Just after first leaf emergence (i.e. after 2 weeks), seedlings were transferred for one week into a plastic tank (20L) containing the nutrient solution described above. Natural light was supplied by high pressure sodium lamps (Philips, MASTER GreenPower T400W) with a PAR (Photosynthetically Active Radiations) of 450 µmol photons.m-2.s-1 at canopy height. At the emergence of the fourth leaf, silicon (Si) pretreatment was applied for one week (Fig. 1). For this, plants were separated into two groups: the first (+Si) was supplied with the nutrient solution described above with the addition of 1.7 mM silicon (Si as sodium metasilicate: Na2SiO3·9H2O) and the second (-Si; Control) with the nutrient solution plus NaCl (3.4 mM) to compensate the sodium supplied by sodium metasilicate in the +Si treatment. Nutrient solutions were aerated and renewed every 3 days and their pH was adjusted daily to 5.6 with HCl (or NaOH). After one week of Si treatment, shoot and root were separated and immediately frozen with liquid nitrogen before RNA extraction. Hoagland nutrient solution/20°C (day)/17°C(night)/450 µmol photons.m-2.s-1 at canopy
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| Extracted molecule |
total RNA |
| Extraction protocol |
Root_Si_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Genome_build: transcriptome of Brassica napus; Genomes A+C; 10 chromosomes; Genoscope; Brassica_napus_v4.annotation_v5.gtf; gene_id; exon
Mapping and counts of reads by locus gene (tophat2/bowtie2). If PE reads, count only consistent PE reads
Supplementary_files_format_and_content: type:count file (txt); content:gene ID,length of Gene,nb single reads,nb PE reads
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| Submission date |
Nov 26, 2018 |
| Last update date |
Feb 22, 2019 |
| Contact name |
Véronique BRUNAUD |
| E-mail(s) |
[email protected]
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| Organization name |
INRAE - CNRS - UPSUD
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| Lab |
IPS2
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| Street address |
rue Noetzlin
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| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
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| Platform ID |
GPL25850 |
| Series (1) |
| GSE122968 |
transilice - Effects of silicon (Si) supply on leaf and root transcriptomes |
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| Relations |
| BioSample |
SAMN10482705 |
| SRA |
SRX5063179 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3489346_samcount_Root_Si_2.txt.gz |
321.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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