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| Status |
Public on May 25, 2018 |
| Title |
GEK12 |
| Sample type |
SRA |
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| Source name |
whole flowers
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| Organism |
Glycine max |
| Characteristics |
sample: pool
tissue: whole flowers
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| Growth protocol |
The samples were collected from the soybean cultivar ‘Urano’ grown at the experimental field of University of Passo Fundo (UPF) (Passo Fundo, Brazil) during the R2-R3 soybean developmental stage.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Collected samples were immediately powdered in Trizol (Invitrogen, CA, USA) and stored until the RNA extraction. Total RNA was isolated using Trizol (Invitrogen, CA, USA), and following the manufacturer’s instructions. The RNA quality was evaluated by electrophoresis in 1.0% agarose gel and the amount of the RNA was checked using a Quibit fluorometer and Quant-iT RNA assay kit according to the manufacturer’s instructions (Invitrogen, CA, USA). Approximately 10 µg of total RNA was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing and sequencing using Solexa technology on the Illumina Genome Analyzer GAII. Briefly, the processing by Illumina consisted of the following successive steps: acrylamide gel purification of RNA bands corresponding to the size range 20–30 nucleotides (nt), ligation of 3′ and 5′ adapters to the RNA in two separate subsequent steps each followed by acrylamide gel purification, cDNA synthesis and a final step of PCR amplification to generate DNA colonies template library for Illumina sequencing.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences
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| Submission date |
Jun 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Guilherme Cordenonsi da Fonseca |
| E-mail(s) |
guicf13@gmail.com
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| Organization name |
UFRGS
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| Department |
Centro de Biotecnologia
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| Lab |
LGPP
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| Street address |
Av. Bento Gonçalves, 9500
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| City |
Porto Alegre |
| State/province |
RS |
| ZIP/Postal code |
91501-970 |
| Country |
Brazil |
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| Platform ID |
GPL15087 |
| Series (1) |
| GSE69572 |
Novel and Conserved microRNAs in soybean floral whorls |
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| Relations |
| BioSample |
SAMN03761633 |
| SRA |
SRX1048542 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1704058_GEK-12.tab.gz |
10.7 Mb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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