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Sample GSM3990079 Query DataSets for GSM3990079
Status Public on Aug 01, 2019
Title esg[ts] gut, biological rep3 [e_3]
Sample type SRA
 
Source name Drosophila esg[ts] guts 10 days post activation
Organism Drosophila melanogaster
Characteristics genotype/variation: w; esgGal4, tubGAL80[ts], UASGFP/+;+/+
timepoint: 10 days post activation
tissue: dissected midgut
cell type: progenitor cells
Treatment protocol After the 10 day heat shift, a total of 10 guts per sample (virgin female) were dissected into Trizol and used for RNA extraction.
Growth protocol Flies were raised on regular food (standard cornmeal food) at 18C befor eclosion. Adult flies were transferred to 29C for 10 days to get ImdD30A expression in gut progenitor cells or enterocytes.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Library construction and sequencing was performed by Novogen company.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Basecalls 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
Supplementary_files_format_and_content: counts and edgeR
 
Submission date Jul 31, 2019
Last update date Aug 02, 2019
Contact name Edan Foley
E-mail(s) efoley@ualberta.ca
Organization name University of Alberta
Department Medical Microbiology and Immunology
Lab 659 HMRC
Street address 116 st and 85 ave
City Edmonton
State/province Alberta
ZIP/Postal code T6G2S2
Country Canada
 
Platform ID GPL25244
Series (1)
GSE135154 Expression data from D. melanogaster guts with suppression of Imd in progenitors or enterocytes
Relations
BioSample SAMN12404889
SRA SRX6619802

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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