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| Status |
Public on Apr 09, 2017 |
| Title |
GEK90 |
| Sample type |
SRA |
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| Source name |
mature seeds
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| Organism |
Vernicia fordii |
| Characteristics |
sample: pool
daf: 90 to 120
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| Growth protocol |
fruits from V. fordii plants growth in an open environment were collected at 100-120 (mature seeds) days after flower opening (DAF). Seeds were dissected from fruits and immediately frozen in liquid nitrogen and stored at -80 °C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the seed material using Trizol (Invitrogen, CA, USA) according to the manufactures’ protocol, and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing and sequencing by Illumina HiSeq2000. Three libraries were generated from immature, intermediate and mature seeds. Briefly, the polyadenylated transcript sequencing (mRNA-seq) was performed using the following successive steps: Poli-A purification, cDNA synthesis using Poli-T primer shotgun to generate inserts of 500 nt, 3p and 5p adapters ligations, pre-amplification, colony generation and sequencing. The Illumina output data were sequence tags of 100 bases.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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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 |
Apr 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Rogerio Margis |
| E-mail(s) |
[email protected]
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| Organization name |
Universidade Federal do Rio Grande do Sul
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| Department |
Centro de Biotecnologia
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| Lab |
Laboratório de Genomas e Populações de Plantas - LGPP
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| Street address |
Av. Bento Goncalves 9500
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| City |
Porto Alegre |
| State/province |
RS |
| ZIP/Postal code |
91501-970 |
| Country |
Brazil |
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| Platform ID |
GPL17722 |
| Series (1) |
| GSE56652 |
Transcriptome of tung tree sees with emphasis on genes from lipid metabolism |
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| Relations |
| BioSample |
SAMN02724949 |
| SRA |
SRX514731 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1366398_GEK90_unique.txt.gz |
536.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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