|
| Status |
Public on Jun 24, 2016 |
| Title |
Leaf non-infested rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf tissue
|
| Organism |
Hordeum vulgare |
| Characteristics |
Stage: V5-30 days old
leaf number: leaf number 5
mite strain: none
|
| Treatment protocol |
The 5th leaves of 30-day-old barley plants were used for the experiment. Mite movement was restrained by barriers made of a non-toxic wax (TangleFoot). Mites were allowed to feed on both sides of a leaf section defined by TangleFoot barriers. The barley leaf sections were infested with healthy adult females, 400 mites per leaf section for 2hr-timepoints and 200 mites per leaf section for 24hr-timepoints. Wounding treatment was applied by rubbing 60 grit sand paper on both sides of the leaf. The control leaves received the TangleFoot barriers but none of the treatments. Mite infestation and wounding treatments were applied at 24hr and 2hr before sample collection. All samples were collected at the same time to limit the effects of the circadian cycle and any minor environmental differences on gene expression.
|
| Growth protocol |
The barley (Hordeum vulgare, Morex variety) plants used for the experiments were germinated and grown in a growth chamber with 16h-light/8h-dark photoperiod at a temperature of approximately 20 degrees C. They were cultivated using Sun Gro® Metro-Mix® 900 Grower Mix, watered as needed, and fertilized weekly with 200ppm NutriCulture 18N-6P-18K.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Leaf tissue was ground to fine powder in liquid nitrogen. Total RNA was prepared using the DirectZol RNA extraction kit (Zymo Research). Quality of the RNA extractions was assessed using a Bioanalyzer (Aligent).
The libraries were prepared at the University of Utah High Throughput Genomics facility using the Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
11812X4
|
| Data processing |
Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61), a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003), and the resulting reads were aligned to the H. vulgare reference genome (082214) with STAR 2.5.1b in two-pass alignment mode (alignments were independent of the existing reference annotation).
Read counts for genes in the ASM32608v1 annotation were obtained using HTSeq 0.6.0 with --stranded reverse and --feature transcript.
Genome_build: 082214 (genome sequence) and ASM32608v1 (genome annotation) were downloaded from the barley genome site at ensembl.org.
Supplementary_files_format_and_content: Tab-delimited text file with counts of reads per gene from alignments as assessed with HTSeq (expression across all samples is included in the single processed data file).
|
| |
|
| Submission date |
Jun 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard M Clark |
| Organization name |
University of Utah
|
| Department |
Department of Biology
|
| Lab |
Clark Laboratory
|
| Street address |
257 So. 1400 East, RM 204 SB
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL22077 |
| Series (1) |
| GSE83676 |
Barley transcriptional responses to specialist and generalist spider mite herbivores |
|
| Relations |
| BioSample |
SAMN05290739 |
| SRA |
SRX1873529 |
