|
| Status |
Public on Dec 31, 2016 |
| Title |
B12-1 |
| Sample type |
SRA |
| |
|
| Source name |
stem tissues
|
| Organism |
Solanum tuberosum |
| Characteristics |
tissue: stem
cultivar: BP1
phenotype: tolerant
inoculant: Pectobacterium carotovorum subsp brasiliense 1692
|
| 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)
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 and normal 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
HTSeq-count was used to make read counts mapped to lncRNA transcripts and DeSeq2 was used to determine the differential expression with a false discovery rate threshold of 10%
Genome_build: PGSC_DM_v4.03
|
| |
|
| Submission date |
Nov 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stanford Kwenda |
| E-mail(s) |
stankwenda@gmail.com
|
| 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) |
| GSE74870 |
Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Time-course RNAseq] |
| GSE74871 |
Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection |
|
| Relations |
| BioSample |
SAMN04254445 |
| SRA |
SRX1426103 |
