|
| Status |
Public on Aug 29, 2018 |
| Title |
CTRL_49_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole spike
|
| Organism |
Hordeum vulgare |
| Characteristics |
cultivar: Golden Promise
tissue: whole spike
developmental stage: BBCH scale - stage 49
genotype: azygous control
|
| Growth protocol |
Plants were sawn in brown-earth soil with a density of 200 plants m-2 in 1.2 x 21 m plots. A mineral fertilizer containing 27% nitrogen was conventionally applied twice during springtime (30 kg per ha). In the vegetation period, plants were treated by herbicide (Mustang Forte) and fungicides (Acanto, Capalo)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3 µg of total RNA from each sample, extracted with RNAqueous kit (Thermo Fischer Scientific, Waltham, USA) and treated with TURBO DNA-free kit (Thermo Fischer Scientific, Waltham, USA) was used for cDNA library preparation by Illumina® TruSeq® Stranded mRNA Sample Preparation Kit (Illumina, Madison, USA).
cDNA library was prepared by Illumina® TruSeq® Stranded mRNA Sample Preparation Kit (Illumina, Madison, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
DESeq_norm_all_counts.csv
|
| Data processing |
The reads were mapped to the reference genome of Hordeum vulgare (Hordeum_082214v1.30) by STAR aligner (STAR_2.4.2a)
Reads quantification was processed by subread-1.5.2 against GTF/GFF file (Hordeum_vulgare.082214v1.30.gtf)
Normalized counts were obtained by DESeq2 normalization
Genome_build: Hordeum_082214v1.30
Supplementary_files_format_and_content: DESeq2 normalized counts
|
| |
|
| Submission date |
Aug 28, 2018 |
| Last update date |
Aug 29, 2018 |
| Contact name |
Petr Vojta |
| Organization name |
Palacky University
|
| Department |
Laboratory of experimental medicine
|
| Street address |
Hnevotinska 5
|
| City |
Olomouc |
| ZIP/Postal code |
77900 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL22077 |
| Series (1) |
| GSE119154 |
MODIFICATION OF BARLEY PLANT PRODUCTIVITY THROUGH REGULATION OF CYTOKININ CONTENT BY REVERSE-GENETICS APPROACHES |
|
| Relations |
| BioSample |
SAMN09928140 |
| SRA |
SRX4618941 |
