|
| Status |
Public on May 24, 2024 |
| Title |
AP1_blocked_ctrl_42d_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole brains
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole brains
genotype: repoGS>UAS-GFP
treatment: RU-486 1d/wk
biological replicate: 3
age: 42d
|
| Treatment protocol |
Treatment refers to feeding flies the geneSwitch activating drug RU-486
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extract by trizol/chloroform and Zymo RNA clean and concentrator kit-5 (R1015)
RNA libraries for FACS sorted cells were prepred by Admera, using SMART-Seq V4 and NexteraXT Library Preparation. RNA lirbaries for whole brains were prepared by Admera, using TruSeq Stranded with Poly-A Selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Demultiplexed reads passing QC filter (Q > 30) were obtained from BaseSpace then merged across sequencing lanes for each sample, with approximately 20 million reads total per sample
Paired-end reads were aligned to the fly genome using HISAT2 (v2.1.0)
The HISAT2 index was built from FlyBase’s Drosophila melanogaster reference genome r6.17
Alignment sorted BAM files (samtools v.15) for each sample were merged across sequencing runs (picard)
Reads that uniquely aligned to exonic regions were counted with HTSeq (v0.9.1) with the union setting to produce a count matrix for differential expression analysis
Assembly: FlyBase’s Drosophila melanogaster reference genome r6.17
Supplementary files format and content: tab-seperated text file includes raw counts for each sample
|
| |
|
| Submission date |
Apr 14, 2024 |
| Last update date |
May 24, 2024 |
| Contact name |
Nancy M Bonini |
| E-mail(s) |
nbonini@sas.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Biology
|
| Street address |
433 S University Ave
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE263928 |
Senescent glia link neuronal mitochondrial dysfunction and lipid droplet accumulation with age |
|
| Relations |
| BioSample |
SAMN40963633 |
| SRA |
SRX24245156 |
