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| Status |
Public on Aug 03, 2017 |
| Title |
vrs4.k (GSHO 1986) 1327AR |
| Sample type |
SRA |
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| Source name |
apex tissue
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| Organism |
Hordeum vulgare |
| Characteristics |
developmental stage: Waddington stage 5.5
genetic background: IL in cv. Bowman
phenotype: vrs4.k (GSHO 1986) 1327AR 1327AR
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| Treatment protocol |
No treatment
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| Growth protocol |
Plants were grown under long day conditions (16h, 22°C day; 8h, 18°C night)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Main shoot apex tissue was isolated at Waddington stage W3.5 and 5.5 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
BWA-MEM 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
Genome_build: As reference a combined set public available data of HC and LC predicted coding sequences of barley cv. Morex (The International Barley Genome Sequencing Consortium 2012) was used.
Variant calling was performed with GATK UnifiedGenotyper (Version 3.1-1) on on processed alignment files using a combined set of High Confidence (HC) and Low confidence (LC) predicted coding sequences of barley cv. Morix (TBGC, 2012) as reference.
Supplementary_files_format_and_content: Excel sheet with log fold changes comparing the different states, vcf file with varant information
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| Submission date |
Aug 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kurt Stueber |
| E-mail(s) |
[email protected]
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| Organization name |
Max Planck Institute for Plant Breeding Research
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| Department |
Genome Centre
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| Street address |
Carl von Linne-Weg 10
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| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
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| Platform ID |
GPL22077 |
| Series (1) |
| GSE102191 |
RNA sequencing of Hordeum vulgare near-isogenic lines |
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| Relations |
| BioSample |
SAMN07444164 |
| SRA |
SRX3056740 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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