|
| Status |
Public on Nov 23, 2011 |
| Title |
turt_smrna_embryo |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Tetranychus urticae |
| Characteristics |
strain: London
developmental stage: embryo
tissue: whole body
gender: males and females
|
| 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, embryos and larvae and nymphs were filtered through a series of fine sieves to isolate the various life stages. RNA isolated from larvae and nymphs were combined in equimolar amounts for the generation of a pooled larvae/nymph small RNA library.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries construction was contracted out to Fasteris SA. Barcoded smRNA libraries were constructed according to their protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Small RNA
|
| Data processing |
The original small RNA fastq file was split by barcode allowing up to one mismatch for the respective samples, and adaptor sequences were removed (trimming was performed by Fasteris SA). Afterwards, reads of lengths from 18-28 nucleotides were mapped to the 12/10/2010 release of the spider mite (Tetranychus urticae) genome using MAQ (up to ten matches were allowed to the genome).
|
| |
|
| Submission date |
Sep 08, 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) |
| GSE32005 |
Developmental stage-specific small RNA composition in the two-spotted spider mite (Tetranychus urticae) |
| GSE32342 |
The genome of Tetranychus urticae reveals herbivorous pest adaptations |
|
| Relations |
| SRA |
SRX096451 |
| BioSample |
SAMN00716198 |
