|
Status |
Public on Oct 07, 2019 |
Title |
Ecc15_4h_1 |
Sample type |
SRA |
|
|
Source name |
Adult fly gut
|
Organism |
Drosophila melanogaster |
Characteristics |
strain: w1118 treatment: Ecc15_4h
|
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 |
S5
|
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 |
SAMN11160969 |
SRA |
SRX5537921 |