|
| Status |
Public on Jun 02, 2020 |
| Title |
WC-3 |
| Sample type |
SRA |
| |
|
| Source name |
abdomenal tissue from pool of 1 flatwing and 1 normal-wing individual
|
| Organism |
Teleogryllus oceanicus |
| Characteristics |
population: Kauai
tissue: abdomenal tissue from pool of 1 flatwing and 1 normal-wing individual
time since infestation: uninfested
|
| Treatment protocol |
Within 48 hours of arrival at UMN, first instar O. ochracea planidia were dissected from gravid female flies. Sexually mature adult male crickets were manually infested with two planidia by transferring them on the tip of a dissecting probe onto the body of the cricket under the junction between the thorax and the abdomen. Crickets were then returned to the incubator in their individual containers and left undisturbed for 24 hours. Crickets in the uninfested control group were handled in an identical manner and for the same amount of time, except that no larvae were transferred on the probe.
|
| Growth protocol |
Cricket lab colonies were housed in groups of 25-40 adults in 15L containers in temperature, humidity, and light controlled incubators set at 26°C and 75% humidity with a 12:12 photoreversed light:dark schedule. Juvenile males were removed from their colony prior to their penultimate molt, and transferred to individual 118mL containers containing Teklad high-fiber rabbit chow, a small piece of water-soaked cotton, and egg carton material for shelter. Female flies were captured in the Santa Monica Mountains, Los Angeles County, California using acoustic traps and shipped overnight to the University of Minnesota. Flies were maintained separately from crickets in an incubator at 26°C and 75% humidity with a 12:12 photoreversed light:dark schedule until infestation.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Head and body tissues were separated and the digestive tract discarded. Samples were immediately stored in RNAlater Solution (Ambion) at 4°C for 24 hours. Immediately prior to extraction, pronotum, wings and legs were removed from the bodies; larvae were then dissected from the abdomen. Total RNA was extracted from remaining body tissue using RNeasy Plus kits with gDNA eliminator spin columns (Qiagen) according to the manufacturer’s directions.
Sequencing libraries enriched for mRNA were prepared using the TruSeq RNA Library Preparation Kit v2 (Illumina) at the University of Minnesota Genomics Center (UMGC; Minneapolis, MN).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling and demultiplexing was performed by the University of Minnesota Genomics Center using Illumina software.
Raw reads were filtered and trimmed using Trimmomatic v 0.33. We trimmed low quality sequences when the average score within a sliding window of 4 bp reached Q < 5, as well as removing any Illumina Tru-seq adapter sequences. Reads shorter than 25 bp in length after trimming were discarded. Only sequences for which both reads of a pair passed quality filters were used.
Trimmed reads were aligned to the genome using STAR v 2.5.3a using two-pass alignment. The first mapping pass used default parameters and a reference set of splice junctions. For the second mapping pass, novel splice junctions inferred from all samples were merged using StringTie v 1.3.4d were used.
Read counts by gene were quantified using STAR --quantMode GeneCounts during the second mapping pass.
Genome_build: Teleogryllus oceanicus genome (Pascoal et al 2019 Evol Let)
Supplementary_files_format_and_content: tab-delimited text files with read counts per gene, output from STAR --quantMode GeneCounts
|
| |
|
| Submission date |
Jun 01, 2020 |
| Last update date |
Jun 02, 2020 |
| Contact name |
Kristin L Sikkink |
| Organization name |
University of Minnesota
|
| Department |
Ecology, Evolution, and Behavior
|
| Lab |
Emilie Snell-Rood
|
| Street address |
1987 Upper Buford Circle
|
| City |
Saint Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL28608 |
| Series (1) |
| GSE151539 |
Immunogenetic and tolerance strategies against a novel parasitoid of wild field crickets |
|
| Relations |
| BioSample |
SAMN15071158 |
| SRA |
SRX8436522 |
