|
| Status |
Public on Oct 07, 2019 |
| Title |
myo>UASlark_Control_4h_3 |
| Sample type |
SRA |
| |
|
| Source name |
Adult fly gut
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: myo>UASlark
treatment: Control
|
| Treatment protocol |
Flies were subsequently infected with Pseudomonas entomophila using the standard oral infection protocol (OD600 nm of 100 and 1.5% sucrose)
|
| Growth protocol |
For specific knockdown or overexpression of lark in the adult gut enterocyte, F1 lines carrying a copy of the MyoIA-Gal4 and tub-Gal80ts transgenes, as well as one copy of either the UAS-IR or the UAS-ORF were kept at 18°C for three days post-eclosion, and then moved to 29°C for 8 days to activate the UAS transgenes.
|
| 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 |
S15
|
| 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 |
| GSE128488 |
RNA-sequencing of the female adult fly guts with enterocyte-specific overexpression and silencing of lark in control and Pseudomonas entomophila infected states. |
|
| Relations |
| BioSample |
SAMN11160929 |
| SRA |
SRX5537913 |
