 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 23, 2020 |
| Title |
mnd1.a 1328AQ |
| Sample type |
SRA |
| |
|
| Source name |
enriched inflorescence material
|
| Organism |
Hordeum vulgare |
| Characteristics |
tissue: inflorescence
developmental stage: Waddington stage 2.0
genetic background: cv. Bowman
genotype: mnd1.a (GSHO2038)
|
| Growth protocol |
Plants were grown under long day conditions (16h, 22°C day; 8h, 18°C night).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Enriched inflorescence tissue was isolated at Waddington stage W2.0, W3.5 and 5.0 and frozen in liquid nitrogen. Tissue was ground, dissolved in 500 mL TRIzol reagent (Invitrogen), incubated for 5 min at room temperature after which, 100 mL of chloroform was added. The sample was homogenized, incubated for 2 min, and centrifuged for 15 min at 4°C followed by phase separation (keeping the aqueous phase). Next, isopropanol was added and incubated for 10 min at room temperature and further purified using an RNA easy Micro Kit (Qiagen). Residual DNA was removed using a DNA-free kit (Ambion). The quality of the RNA was tested using a bio analyzer (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
BWA-MEM (version 0.7.15) was used for alingment of the reads, Salmon was used to extract transcript per million (TPM) values.
Log fold change values comparing mutant versus wildtype at different developmental stages were obtained using Limma-Voom (compare to van Esse et al., 2017).
Variant calling was performed with GATK UnifiedGenotyper (Version 3.6) on processed alignment files (compare to van Esse et al., 2017).
Genome_build: A combined set of High Confidence (HC) and Low confidence (LC) predicted coding sequences of barley cv. Morex (Mascher et al., 2017) as reference was used.
Supplementary_files_format_and_content: Excel sheet with log fold changes comparing the different stages, vcf file with variant information.
|
| |
|
| Submission date |
Apr 22, 2020 |
| Last update date |
Apr 23, 2020 |
| Contact name |
Agatha Alexandra Walla |
| Organization name |
Heinrich-Heine-University
|
| Department |
Institut of Plant Genetics
|
| Street address |
Universitätsstraße 1
|
| City |
Düsseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22077 |
| Series (1) |
| GSE149110 |
RNA sequencing of the Hordeum vulgare near-isogenic line mnd1.a |
|
| Relations |
| BioSample |
SAMN14668619 |
| SRA |
SRX8155495 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
