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| Status |
Public on Jan 26, 2022 |
| Title |
WD_t1_50_3 |
| Sample type |
SRA |
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| Source name |
WD_t1_50_3
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| Organism |
Brassica napus |
| Characteristics |
treatment: WD_t1_50
genotype: wild type (Trezzor)
developmental stage: planting-date=05-JUN-19,harvest-date=10-JUL-19
tissue: leaf
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| Treatment protocol |
water shortage-environmental treatment-water shortage,abiotic stress-water deficit In a greenhouse, 30 days after sowing with a growth at 80% field capacity (FC) level, irrigation was kept for control or was stopped until all pots per condition reached a level below 50% of FC (harvest t1_50) and thereafter 25% FC (harvest t1_25). Once theses levels were reached, plant were kept respectively at 50% FC or 25% FC during 12 days before final harvest (havest t2_ 50 and t2_25 respectively). Each harvest consisted to sample leaf blade which has been growing during water shortage for the control condition and the water deficient condition.
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| Growth protocol |
Controled conditions (greenhouse) Media: PremierTech sandy compost Hygrometry: 80% field capacity (Fc) Temperature: 25°C day / 20°C night Light: 500 µmol.m².s-1
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| Extracted molecule |
total RNA |
| Extraction protocol |
WD_t1_50_3(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.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: genome of Brassica napus
genome mapping and counts of reads by gene locus are done with STAR; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts_noStranded,counts_forwardStrand,counts_reverseStrand
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| Submission date |
Jun 28, 2021 |
| Last update date |
Jan 26, 2022 |
| 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) |
| GSE179022 |
eauptic one-Effet of water shortage on the whole foliar elemental content (ie. Ionome) |
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| Relations |
| SRA |
SRX11242983 |
| BioSample |
SAMN19945832 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5403797_STARcount_WD_t1_50_3.txt.gz |
485.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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