|
| Status |
Public on Apr 21, 2021 |
| Title |
ecd1_3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: ecd1
condition: 18 °C for 10 days, upshifted to 29°C for 2 days
tissue: Whole larvae
|
| Treatment protocol |
w1118 and ecd1 larvae grown at 18 °C for 10 days were upshifted to 29 °C for 2 days.
|
| Growth protocol |
w1118 and ecd1 larvae were grown at 18 °C for 10 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from eight third instar larvae using the standard protocol with TRI Reagent and DNase I treatment.
RNA libraries were generated according to the Illumina protocol and pair-end sequenced on an Illumina HiSeq 2000 instrument at 100 bp read length. Image analysis and base calling were done with the Illumina RTA software at run time.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calling were done with the Illumina RTA software at run time
Reads were aligned to the Drosophila reference genome BDGP Release 6 (dm6) using Tophat2 v2.0.10
Mapped reads summarization was performed on the gene meta-feature level using featureCounts v1.6.4
Differential gene expression was assessed using DESeq2
Differential splicing events were determined using LeafCutter algorithm.
Genome_build: BDGP Release 6 (dm6)
Supplementary_files_format_and_content: .xlsx file containing sheet summary, QCR report, Lists of differentially regulated genes and their DESeq2 normalized counts, Enriched GO terms for up- and downregulated genes in ecd1 condition, and List of differentially spliced genes in ecd1 condition
|
| |
|
| Submission date |
Apr 21, 2020 |
| Last update date |
Apr 21, 2021 |
| Contact name |
Mirka Uhlirova |
| E-mail(s) |
mirka.uhlirova@uni-koeln.de
|
| Organization name |
CECAD Research Center Cologne
|
| Department |
Institute for Genetics
|
| Lab |
Uhlirova Lab
|
| Street address |
Joseph-Stelzmann Str. 26
|
| City |
Cologne |
| State/province |
NRW |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE149056 |
Assessment of changes in gene expression and splicing in ecd1 homozygous mutant third-instar larvae kept at restrictive temperature (29°C) |
|
| Relations |
| BioSample |
SAMN14655842 |
| SRA |
SRX8151460 |
