|
| Status |
Public on Oct 31, 2023 |
| Title |
D melanogaster, M luteus injected, 3 hours, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole male Drosophila melanogaster
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole male Drosophila melanogaster
genotype: w[1118] ; c564 / +
|
| Treatment protocol |
Bacteria were injected as suspensions in PBS at OD600=1. Flies were then kept at 29° for 3 hours before being homogenized in TRIzol for RNA extraction.
|
| Growth protocol |
Drosophila melanogaster were kept on 10% yeast, 8% fructose, 2% polenta, 0.8% agar, supplemented with nipagin and propionic acid. Bacteria were cultured in LB.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol (Life Technologies) was used according to the manufacturer's instructions.
Libraries were prepared using Illumina TruSeq Stranded mRNA v2, with the following changes from the manufacturer’s protocol: starting samples were 250ng total RNA; fragmentation was performed for 10 minutes at 94°; no spike-ins were used; and 14 cycles of PCR were used to enrich libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Libraries were sequenced on an Illumina NextSeq 500 using v1 chemistry.
|
| Data processing |
Reads were assigned to transcripts (Flybase Dmel 6.33) using Kallisto 0.46.1
Transcript assignments were converted to genes and differentially expressed genes were identified using Sleuth
Assembly: FlyBase release 6.33
Supplementary files format and content: wt_gene-level_TPMs_6.33.csv is a csv showing TPM (transcripts per million) values for each gene in each sample, generated using Kallisto and Sleuth. Genes are listed with two identifiers, a gene name and a FlyBase identifier (FBGn).
|
| |
|
| Submission date |
Oct 18, 2022 |
| Last update date |
Oct 31, 2023 |
| Contact name |
Marc Dionne |
| E-mail(s) |
[email protected]
|
| Organization name |
Imperial College London
|
| Department |
Life Sciences
|
| Street address |
Level 0, Flowers Building
|
| City |
London |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE216042 |
Gene expression in Drosophila melanogaster in response to bacterial infection |
|
| Relations |
| BioSample |
SAMN31355958 |
| SRA |
SRX17942478 |
