|
| Status |
Public on Aug 01, 2019 |
| Title |
Myo1A[ts] gut, biological rep1 [M_1] |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila Myo1A[ts] guts 10 days post activation
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: w; Myo1AGal4/+; tubGAL80[ts], UASGFP/+
timepoint: 10 days post activation
tissue: dissected midgut
cell type: enterocytes
|
| 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 |
SAMN12404885 |
| SRA |
SRX6619806 |
