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| Status |
Public on Oct 24, 2016 |
| Title |
F039 |
| Sample type |
SRA |
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| Source name |
whole seedling
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| Organism |
Zea mays |
| Characteristics |
genetic background: inbred line
tissue: whole seedling
age: 7 days after germination
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| Growth protocol |
Five biological replicates of each genotype (Sample 1-25) were grown in a climate chamber (Percival Scientific Inc., Perry, USA) under controlled conditions (25°C, 16h day, 8h night, 70% air humidity) for seven days, flash-frozen in liquid nitrogen, and pooled before RNA isolation. For Sample 26-31 nucellus tissue of P1/HC-Pro x H99 hybrids were isolated one day after pollination (dap) and transfered to plates with modified MS-medium. The transgenic viral suppressor was induced via 20 µM Dexamethasone to the medium, half of the plates was mock-treated with ethanol. Two days after germination (dag) the tissue was transfered into glass containes containing standard MS media and either Dexamethasone or ethanol. Whole seedlings were harvested 20 dag, flash-frozen in liquid nitrogen and stored until RNA isolation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation of all samples was performed using the miRVana miRNA Isolation Kit (Life technologies Corp., Carlsbad, USA).
sRNA sample library preparation was performed using the TruSeq SBS Kit v5 (Illumina Inc., San Diego, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 3
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| Data processing |
Basecalls were performed using CASAVA (version 1.7 for samples 1-3,5-22; version 1.8.1 for samples 23-24; version 1.8.2 for sample 4,25-31).
Raw reads were trimmed from adapter and low quality nucleotide reads (<99.9%) using a custom Java program, all reads within 15-nt to 40-nt were retained and identical sequences merged to obtain raw read counts.
Read counts of samples 1-25 (“association_srna”) were quantile normalized and scaled to 1 Mio. normalized reads per library (qnrpm). Raw read counts of samples 26-31 („p1_hc-pro_suppressor“) were used for analyses.
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| Submission date |
Oct 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Scholten |
| E-mail(s) |
stefan.scholten@uni-hamburg.de
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| Phone |
0049 40 42816329
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| Organization name |
University of Hamburg
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| Department |
Biocenter Klein Flottbek
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| Lab |
Developmental Biology and Biotechnology
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| Street address |
Ohnhorststrasse 18
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| City |
Hamburg |
| ZIP/Postal code |
22609 |
| Country |
Germany |
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| Platform ID |
GPL15463 |
| Series (1) |
| GSE51662 |
Distinct small RNA populations act antagonistically in formation of heterosis |
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| Relations |
| BioSample |
SAMN02383989 |
| SRA |
SRX367606 |
| 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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