|
| Status |
Public on Oct 07, 2019 |
| Title |
Control_16h_1 |
| Sample type |
SRA |
| |
|
| Source name |
Adult fly gut
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w1118
treatment: Control_16h
|
| Treatment protocol |
Flies were starved for 2 hours at 29 degrees, then were either fed 1.5X sucrose (control) or Pseudomonas entomophila (OD600nm = 100) or Erwinia carotovora carotovora 15 (OD600nm = 100).
|
| 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.
Paired-end Illumna stranded Truseq libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
S2
|
| Data processing |
Base-calls performed using CASAVA version 1.4
Reads were trimmed with Trim Galore version 0.4.1 with the --paired option and default parameters
Sequencing reads were mapped to the Dm3 reference genome sequence.
The Ensemble GTF file from BDGP5.25 was used as a starting file for annotations.
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.
Supplementary_files_format_and_content: count
|
| |
|
| Submission date |
Mar 18, 2019 |
| Last update date |
Oct 07, 2019 |
| Contact name |
Maroun Bou Sleiman |
| E-mail(s) |
maroun.bousleiman@epfl.ch
|
| Organization name |
EPFL
|
| Department |
IBI
|
| Lab |
LISP
|
| Street address |
Rue Cantonale
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE118622 |
Enteric infection induces extensive Lark-mediated 5' retention of exon-like introns in Drosophila |
| GSE128489 |
RNA-sequencing of the adult female fly guts (w1118) with and without oral infection with Pseudomonas entomophila (Pe) or Erwinia carotovora carotovora 15 (Ecc15) |
|
| Relations |
| BioSample |
SAMN11160972 |
| SRA |
SRX5537918 |
