|
| Status |
Public on May 27, 2016 |
| Title |
drought_baw1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf_drought_baw
|
| Organism |
Solanum dulcamara |
| Characteristics |
water treatment: drought
insect treatment: 48-h herbivory by Spodoptera exigua (BAW)
tissue: leaf
|
| Treatment protocol |
5 days water treatments + 2 days insect treatments, water treatments were maintained during insect treatments
|
| Growth protocol |
plants were grown in standard greenhouse
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of the following tissues was isolated with the Plant RNeasy kit (Qiagen). DNase treatment done using TURBO DNA-free kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data column: 10
|
| Data processing |
read mapping by bowtie v. 0.12.7
Global normalization among samples was performed by the method implemented in the R-package DESeq
Reads per kilobase of contig length per million mapped reads (RPKM) values were also calculated and used to filter out noise contigs with RPKM lower than 1 in all samples
Differential expression calls, based on normalized read counts, were performed using the DESeq
false discovery rate (FDR) p values calculated according to the Benjamini & Hochberg procedure
Genome_build: Solanum dulcamara transcriptome DAgostino2013 Contigs, solgenomics.net
Supplementary_files_format_and_content: each file is a matrix of contig numbers and their raw (or normalized) read counts in each sample
|
| |
|
| Submission date |
Jun 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Duy Nguyen |
| E-mail(s) |
nguyenmduy@gmail.com
|
| Phone |
+31611377444
|
| Organization name |
Radboud University
|
| Department |
Molecular Plant Physiology
|
| Street address |
Heyendaalseweg 135
|
| City |
Nijmegen |
| ZIP/Postal code |
6525AJ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL20294 |
| Series (1) |
| GSE69648 |
Effects of Drought and Flooding on Herbivore-Triggered Transcriptomic Response in Solanum dulcamara |
|
| Relations |
| BioSample |
SAMN03764727 |
| SRA |
SRX1053380 |
