|
| Status |
Public on Aug 15, 2019 |
| Title |
C1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Brassica oleracea |
| Characteristics |
tissue: leaf
treatment: Control
days post-inoculation: 3
ecotype: Early Big (B. oleracea var. italica)
|
| Treatment protocol |
Plants at six leaf stage were inoculated at the third leaf following the method described by Taylor (2002). Control plants were mock-inoculated following the same procedure
|
| Growth protocol |
The doubled haploid broccoli line “Early Big” (B. oleracea var. italica) was used in this study. Plants were sown in plastic pots containing Sphagnum peat (GRAMOFLOR GmbH & Co, Germany) in a greenhouse with a minimum temperature of 20 ºC day and 15°C night venting at 25°C and 60% of humidity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Individual sample tissues were grounded in liquid nitrogen and total RNA from three biological replicates of each treatment was extracted using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich, MO, USA)
Massive Analysis of 3′-cDNA Ends (MACE) was performed from each sample (GenXPro GmbH, Frankfurt am Main, Germany) as described by Zawada et al. (2014)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: MACE
HCS from Illumina HiSeq 2000
Assemblies were performed with NovoAlign v3.00.05; reads mapping to multiple locations were limited to 10
Differential expression analysis was performed with the R package DESeq (Anders and Huber 2010) with the standard parameters
Genome_build: ENSEMBL Brassica oleracea (v2.1), UniProtKB/Swiss-Prot, UniProtKB and Ref-Seq
Supplementary_files_format_and_content: tab-delimited text files including Gene annotation, Expression values, logFC and FDR
|
| |
|
| Submission date |
Dec 05, 2017 |
| Last update date |
Aug 15, 2019 |
| Contact name |
Maria Tortosa |
| E-mail(s) |
[email protected]
|
| Organization name |
Mision Biologica de Galicia (MBG-CSIC)
|
| Street address |
Pazo de Salcedo nº8
|
| City |
Pontevedra |
| State/province |
Galicia |
| ZIP/Postal code |
36143 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16360 |
| Series (1) |
| GSE107720 |
Transcriptomic analysis of Brassica oleracea challenged with Xanthomonas campestris pv. campestris |
|
| Relations |
| BioSample |
SAMN08134392 |
| SRA |
SRX3445623 |
