|
| Status |
Public on Jun 21, 2021 |
| Title |
Line 47 rep.3 periderm |
| Sample type |
SRA |
| |
|
| Source name |
potato tuber skin (periderm)
|
| Organism |
Solanum tuberosum |
| Characteristics |
tissue: tuber periderm
genotype: StRIK-RNAi transgenic line 47
growing conditions: in soil under long-day conditions (12 h light/12 h dark)
|
| Growth protocol |
in soil under long-day conditions (12 h light/12 h dark)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified by means of the PureLink® Plant RNA Reagent (Ambion) using a modification of the standard protocol by repeating twice the step four and five of the protocol and adding a KOAc 2M (pH 5.5) precipitation step to remove polysaccharides. Final RNA precipitation was performed with the GlycoBlue™ Coprecipitant (Ambion). Genomic DNA was removed using TURBO DNA-free kit (Ambion) according to the manufacturer’s instructions.
The cDNA libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Line 47 rep.3
|
| Data processing |
RNA-seq data were first analysed for quality control with FastQC v0.11.2
The reads were aligned with Bowtie 2 (Langmead and Salzberg, 2012) against the S. tuberosum Group Phureja transcriptome generated from the genome assembly v4.03 (Potato Genome Sequencing Consortium et al., (2011) using the most recent version of the GFF3 genome annotation file (PGSC_DM_V403_genes.gff.zip) with the program gffread from the Cufflinks package
The quantification of transcript abundance was performed with eXpress 1.5.1
The eff_counts obtained from eXpress were passed as input to baySeq (Hardcastle et al., 2010) for the differential expression analysis. Transcripts with a likelihood ≥ 0.8 in the specified model and a False Discovery Rate (FDR) lower than 0.05 were considered as differentially expressed
Genome_build: PGSC v4.03 pseudomolecule
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 01, 2020 |
| Last update date |
Jun 21, 2021 |
| Contact name |
Olga Serra |
| E-mail(s) |
[email protected]
|
| Organization name |
Universitat de Girona
|
| Department |
Biologia
|
| Lab |
Laboratori del Suro
|
| Street address |
C/ Maria Aurèlia Capmany, 40
|
| City |
Girona |
| State/province |
Girona |
| ZIP/Postal code |
17003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16436 |
| Series (1) |
| GSE153641 |
The transcriptome of StRIK-silenced periderms suggests a role of this potato gene in RNA processing and stress |
|
| Relations |
| BioSample |
SAMN15418144 |
| SRA |
SRX8648400 |
