|
| Status |
Public on Nov 23, 2016 |
| Title |
V-01 |
| Sample type |
SRA |
| |
|
| Source name |
stem tissues
|
| Organism |
Solanum tuberosum |
| Characteristics |
tissue: stem
cultivar: Valor
phenotype: susceptible
|
| Treatment protocol |
Stem inoculations were done as previously described in (Kubheka et al 2013), except that we used wild-type P. carotovorum subsp. brasiliense strain 1692 for the inoculations and inoculated plants were assessed and sampled at 0, 6, 12, 24, and 72 hours post inoculation (hpi) in triplicates (three plants were pooled together for each biological replicate)
|
| Growth protocol |
Potato tubers were grown in the greenhouse under standard conditions (22 to 26 °C, 16 h light/ 8 h dark photoperiod and 70% relative humidity)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from potato stems using the QIAGEN RNeasy plant mini kit (Qiagen) including DNAse treatment (Qiagen). For the preparation of strand-specific libraries, total RNA was was pooled from five time-points(0, 6,12,24,72 hours post inoculation; hpi) for cultivars BP1 and Valor.
The construction of whole transcriptome libraries and sequencing were carried out at the Beijing Genomics Institute (BGI-Shenzhen, China). cDNA libraries were sequenced using standard Illumina protocols for strand-specific RNA-seq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling and adapter sequence removal were done at BGI-Shenzhen
Strand-specific sequencing reads for each cultivar were quality checked using FASTQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) and mapped to the potato reference genome (Genome assembly: PGSC_DM_v4.03; http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml) using TopHat2 (version 2.0.13)
Transcript assembly was performed using Cufflinks (version 2.2.1)
Coding Potential Calculator (CPC) was used to differentiate candidate lncRNA transcripts from mRNAs
InterproScan used as an additional filter to remove all candidate lncRNA transcripts with similarities to protein domains and signatures in the InterPro database
Genome_build: PGSC_DM_v4.03
Supplementary_files_format_and_content: txt files containing read counts for lncRNAs
|
| |
|
| Submission date |
Nov 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stanford Kwenda |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pretoria
|
| Department |
Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)
|
| Lab |
9-5 New Agricultural Building
|
| Street address |
Lunnon Road, Hilcrest
|
| City |
Pretoria |
| State/province |
Gauteng |
| ZIP/Postal code |
0028 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL16436 |
| Series (2) |
| GSE74869 |
Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Strand-specific RNA-seq] |
| GSE74871 |
Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection |
|
| Relations |
| BioSample |
SAMN04254463 |
| SRA |
SRX1426094 |
