|
| Status |
Public on Aug 01, 2020 |
| Title |
control_BRGC-2 |
| Sample type |
SRA |
| |
|
| Source name |
Brain-ring gland complex
|
| Organism |
Drosophila melanogaster |
| Characteristics |
background strain: w[1118]
genotype: Dfr/vvl[14]
treatment: untreated
|
| Growth protocol |
Larvae were reared at 25 degrees C at 60 % rel. Humidity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using a HiSeq2500 (Illumina TruSeq Stranded mRNA) with Poly-A selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
fastq files were aligned to Ensembl release 95 of Drosophila melanogaster reference genome BDGP6 using STAR after being trimmed with TrimGalore
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Transcripts with average counts below 1 in at least one group were filtered out using the keep function in the edgeR package in R
Expression data was normalized using the calcNormFactors function in the edgeR package in R
Common dispersion and tagwise dispersions were estimate in one run using the estimateDisp function in edgeR
Differentially expressed genes (5% false discovery rate) in BRGC and body were identified by separate analyses using Exact test in edgeR.
Genome_build: Ensembl release 95 of Drosophila melanogaster reference genome BDGP6
Supplementary_files_format_and_content: Excel file includes normalized gene counts and counts adjusted to zero baseline for each sample, exact test and annotation
|
| |
|
| Submission date |
May 06, 2020 |
| Last update date |
Aug 01, 2020 |
| Contact name |
Bo G Lindberg |
| E-mail(s) |
[email protected]
|
| Organization name |
Stockholm University
|
| Department |
MBW
|
| Lab |
Engstrom lab
|
| Street address |
Svante Arrhenius väg 20 C
|
| City |
Stockholm |
| ZIP/Postal code |
106 91 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE149972 |
Stop codon readthrough of a POU transcription factor regulates steroidogenesis and developmental transitions |
|
| Relations |
| BioSample |
SAMN14842796 |
| SRA |
SRX8271844 |
