 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 17, 2021 |
| Title |
Carence_Ca_2 |
| Sample type |
SRA |
| |
|
| Source name |
Carence_Ca_2
|
| Organism |
Brassica napus |
| Characteristics |
genotype: wild type (Trezzor)
developmental stage: planting-date=15-FEB-19,harvest-date=28-MAR-19
tissue: roots
|
| Treatment protocol |
Ca nutriment deprivation-nutriment deprivation,environmental treatment-nutriment deprivation,abiotic stress-calcium This experiment used oilseed rape (Brassica napus cv. Trezzor) grown in hydroponic conditions in a greenhouse (20°C day / 15°C night) at the University de Caen-Normandie (France) between February-March. Seeds were germinated on perlite over demineralized water for five days in the dark and then placed two days under natural light. After the first leaf appearance (BBCH 11 stage), ten seedlings were transferred par 10L plastic container (400 x 300 x 115 mm) with natural light supplemented with high-pressure sodium lamps (HPS 400 Watt, Hortilux Schréder, Monster, Netherlands) at 350 μmol m-2 s-1 of photosynthetically active radiation at the canopy height under 16h day / 8h night photoperiod. After 24 days of growth with complete nutrient solution, plants were separated in 9 subsets. Control plants were kept with the same nutrient solution. Each of the others subsets received a specific solution deprived of a unique element: N, Mg, P, S, K, Ca, Cl, Mn, or Co.
|
| Growth protocol |
Media : control nutrient solution Hygrometry : hydroponics Temperature : 25°C day / 20°C night Light : 350 μmol m-2 s-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Carence_Ca_2(200mg)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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
|
| |
|
| Submission date |
Jul 19, 2021 |
| Last update date |
Nov 17, 2021 |
| Contact name |
Véronique BRUNAUD |
| E-mail(s) |
[email protected]
|
| Organization name |
INRAE - CNRS - UPSUD
|
| Lab |
IPS2
|
| Street address |
rue Noetzlin
|
| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
| |
|
| Platform ID |
GPL25850 |
| Series (1) |
| GSE180378 |
eauptic_carences - Characterization of the ionomic signatures of plants submitted to nutritional deficiencies and some potentially involved mechanism |
|
| Relations |
| BioSample |
SAMN20306936 |
| SRA |
SRX11499408 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5461727_STARcount_Carence_Ca_2.txt.gz |
522.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
