|
| Status |
Public on Jun 01, 2023 |
| Title |
T26R-yki |
| Sample type |
SRA |
| |
|
| Source name |
adult thorax
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-yki-act
tissue: thorax
time course: day26 recover
|
| Treatment protocol |
Eclosed male flies were incubated at 29°C for tumor induction and then shifted back to 18°C for tumor shutdown
|
| Growth protocol |
Crosses were kept at 18°C to avoid expression of yki during development. Adult males were collected every 24-48 hours and incubated at 29°C to induce yki-tumors in the gut. For the recovery phase, flies were incubated at 29°C for 14 days and then shifted back to 18°C for several days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
8-10 thoraces dissected out from the flies either during the tumor induction phase (29°C) or tumor recovery (18°C) and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
rRNA depletion
|
| Data processing |
FastQC was used for sequencing data quality control and MultiQC was used to aggregate the results.
Sequenced reads were aligned to the mm10 reference genome assembly and gene counts were quantified using STAR
Differential gene expression testing was performed by DESeq2
Genome_build: Flybase genome annotation version r6.30
Supplementary_files_format_and_content: text files include read counts for each sample
|
| |
|
| Submission date |
Nov 19, 2021 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Yanhui Hu |
| E-mail(s) |
[email protected]
|
| Phone |
617-432-6546
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Lab |
Norbert Perrimon
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE189214 |
Time course of transcriptomic changes of thoraces comparing wild type and flies with gut yki-tumors during a tumor induction phase and tumor shutdown phase to analyze the recovery of peripheral tissue. |
|
| Relations |
| BioSample |
SAMN23311450 |
| SRA |
SRX13179877 |
