|
| Status |
Public on Sep 11, 2019 |
| Title |
F11259: Unspecific immunity line 5 |
| Sample type |
SRA |
| |
|
| Source name |
20 pooled larvae
|
| Organism |
Tribolium castaneum |
| Characteristics |
tissue: Whole body
priming treatment: Heat-killed Pf
time point: 6h post priming
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pooled larvae were immediately shock frozen in liquid nitrogen and stored at -80oC until further use. RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) according to the protocol of the manufacturer.
The libraries for Illumina sequencing were prepared using the TruSeq RNA sample V2 Kit (Illumina) following the manufacturer’s protocol. The libraries were then clustered on a cBot with the TruSeq PE Cluster Kit V4 (Illumina) with a final loading concentration of 10 pM according to the instructions of the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The quality of the raw reads was first checked with FastQC, after which the first five base pairs were removed using Trimmomatic 0.36 to account for observed biases in sequence composition due to random hexamer priming.
After this filtering step, STAR v2.5.3 was used to map the reads to the Tribolium 5.2 reference genome downloaded from Beetlebase. The mapped reads were then converted from the .sam into the .bam format using
SAM tools v0.1.19 for downstream analyses. The .gff file used for mapping was then converted into a gtf reference file using the “gffread” function of cufflinks v2.2.1. To obtain total gene counts from the mapped reads,
the “htseq-count” function of HTSeq v0.7.2 was used to count by gene ID, after which the individual assemblies were merged into one count table files by means of a custom-made R pipeline.
Genome_build: Tribolium 5.2 reference genome
|
| |
|
| Submission date |
Jul 05, 2019 |
| Last update date |
Sep 11, 2019 |
| Contact name |
Joachim Kurtz |
| E-mail(s) |
joachim.kurtz@uni-muenster.de
|
| Organization name |
University of Münster
|
| Department |
Evolution and Biodiversity
|
| Street address |
Hüfferstraße 1
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18162 |
| Series (1) |
| GSE133892 |
Tribolium castaneum experimental evolution |
|
| Relations |
| BioSample |
SAMN12220826 |
| SRA |
SRX6408780 |
