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Sample GSM1250276 Query DataSets for GSM1250276
Status Public on Oct 24, 2016
Title S058
Sample type SRA
 
Source name whole seedling
Organism Zea mays
Characteristics genetic background: inbred line
tissue: whole seedling
age: 7 days after germination
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.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description Sample 21
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.
 
Submission date Oct 24, 2013
Last update date May 15, 2019
Contact name Stefan Scholten
E-mail(s) [email protected]
Phone 0049 40 42816329
Organization name University of Hamburg
Department Biocenter Klein Flottbek
Lab Developmental Biology and Biotechnology
Street address Ohnhorststrasse 18
City Hamburg
ZIP/Postal code 22609
Country Germany
 
Platform ID GPL15463
Series (1)
GSE51662 Distinct small RNA populations act antagonistically in formation of heterosis
Relations
BioSample SAMN02384013
SRA SRX367624

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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