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Sample GSM4040419 Query DataSets for GSM4040419
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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