|
| Status |
Public on Aug 21, 2019 |
| Title |
esg[ts]/+ whole gut. C6706ΔvasK infected. biological rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila esg[ts]/+ whole guts 24 hour infection
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: dissected whole gut
genotype: w; esgGal4, tubGAL80[ts], UASGFP/+;+/+
infection: C6706[delta]vasK
|
| Treatment protocol |
After 24 hours of infection, for intestinal progenitor cell RNAseq a total of 100 guts per sample (virgin female) were and for whole gut RNAseq 10 guts per sample were dissected into Trizol and used for RNA extraction.
|
| Growth protocol |
Flies were raised on standard cornmeal food at 18C before eclosion. Adult flies were transferred to 29C for 5 days to permit establishment of the adult microbiome. Flies were then mock infected or infected with Vibrio cholerae for 24hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
For intestinal progenitor cell RNAseq, library construction and sequencing was performed by the Lunenfeld-Tanenbaum Research Institute. For whole gut RNAseq, library construction and sequencing was performed by Novogene: genome sequencing company.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calls performed using Cyberduck(FTP)
FASTQC was used to evaluate the quality of raw paired-end sequencing reads. Adaptors and reads of less than 36 base pairs in length were trimmed from the raw reads using Trimmomatic. Reads were aligned to the Drosophila transcriptome- bdgp6 with HISAT2 (version 2.1.0). The resulting BAM files were converted to SAM flies using Samtools (version 1.8).
The converted files were counted using Rsubread (version 1.24.2) and loaded into EdgeR. In EdgeR, genes with counts less than 1 count per million were filtered and libraries were normalized for size. Normalized libraries were used to call genes that were differentially expressed among treatments.
Genome_build: Drosophila transcriptome- bdgp6
|
| |
|
| Submission date |
Aug 20, 2019 |
| Last update date |
Aug 22, 2019 |
| Contact name |
Edan Foley |
| E-mail(s) |
efoley@ualberta.ca
|
| Organization name |
University of Alberta
|
| Department |
Medical Microbiology and Immunology
|
| Lab |
Foley Lab
|
| Street address |
114th St and 87th ave
|
| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2E1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE136069 |
Expression data from D. melanogaster whole guts or intestinal progenitor cells isolated from flies mock infected or infected with wild type Vibrio cholerae (C6706) or type VI secretion system deficient Vibrio cholerae (C6706ΔvasK) |
|
| Relations |
| BioSample |
SAMN12610311 |
| SRA |
SRX6744076 |
