|
| Status |
Public on Oct 07, 2019 |
| Title |
DGRP-301_Infected |
| Sample type |
SRA |
| |
|
| Source name |
Adult fly gut
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: DGRP-301
infection: Pseudomonas entomophila
developmental stage: adult
tissue: fly gut
|
| Treatment protocol |
Flies were starved for 2 hours at 29 degrees, then were either fed 1.5X sucrose (control) or Pseudomonas entomophila OD600nm = 100 (infected)
|
| Growth protocol |
Female adult flies (2-3 days post-eclosion) were reared at 25 degrees C until treatment.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For each condition, guts from 30 adult female flies were collected in PBS four hours post treatment and directly homogenized in trizol (Invitrogen) using a bead-beater. A standard protocol for RNA extraction was performed.
Illumina stranded Truseq libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
s42
|
| Data processing |
Base-calls performed using CASAVA version 1.4
Sequencing reads were mapped to individualized genomes generated using the Dm3 genome sequence and the DGRP freeze 2 genotyping data.
The Ensemble GTF file from BDGP5.25 was used as a starting file for annotations. We used the genotype data, namely indels from the DGRP freeze 2 genotypes to generate individualized GTF files using offsetGTF from the mmseq package.
STAR aligner version 2.3.0 was used to map the reads to individualized genomes.
Htseq-count version 0.5.4p3 was for generating the count tables.
Genome_build: Dm3
Supplementary_files_format_and_content: count table
|
| |
|
| Submission date |
Aug 06, 2018 |
| Last update date |
Oct 07, 2019 |
| Contact name |
Maroun Bou Sleiman |
| E-mail(s) |
[email protected]
|
| Organization name |
EPFL
|
| Department |
IBI
|
| Lab |
LISP
|
| Street address |
Rue Cantonale
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE118142 |
RNA-sequencing of the female adult fly guts from 38 DGRP lines with and without oral infection with Pseudomonas entomophila |
| GSE118622 |
Enteric infection induces extensive Lark-mediated 5' retention of exon-like introns in Drosophila |
|
| Relations |
| BioSample |
SAMN09768046 |
| SRA |
SRX4510307 |
