|
| Status |
Public on Nov 23, 2011 |
| Title |
nymph_techrep2 |
| Sample type |
SRA |
| |
|
| Source name |
nymph
|
| Organism |
Tetranychus urticae |
| Characteristics |
strain: London
developmental stage: nymph
gender: males and females
host: bean
technical replicate: 2
|
| Treatment protocol |
None.
|
| Growth protocol |
Animals were mass reared on bean plants (Phaseolus vulgaris cv California Red Kidney) in growth chambers at 27C with a 16:8 hour (light/dark) photoperiod. Plants were washed in 0.1% TRITON X detergent solution in 2-liter beakers to release all spider mite life stages. Adult spider mites, nymphs, larvae and eggs were filtered through a series of fine sieves to isolate the various life stages.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were generated with methods adapted from the Illumina mRNA sample preparation protocol (cat. no 1004894 Rev.A).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
polyA RNA
r22_l7_nymph_techrep2
|
| Data processing |
Reads were mapped to the spider mite genome using the bowtie/tophat software package. Only unique read mappings were allowed, and genic regions overlapping with other gene models were additionally removed from the gene expression calculations due to the lack of strand specificity. SAM alignment files were parsed using custom python scripts to generate RPKM values based on the 12/10/2010 annotation of the mite genome.
|
| |
|
| Submission date |
Aug 18, 2011 |
| 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 |
GPL14176 |
| Series (2) |
| GSE31527 |
Developmental stage-specific gene expression in the two-spotted spider mite (Tetranychus urticae) |
| GSE32342 |
The genome of Tetranychus urticae reveals herbivorous pest adaptations |
|
| Relations |
| SRA |
SRX092413 |
| BioSample |
SAMN00710359 |
