|
| Status |
Public on Aug 17, 2020 |
| Title |
Old fly brain - rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Brain
age: 70 days
internal name: 191029.HFLFFBGXC.b0706
|
| Growth protocol |
y1w* flies were raised at 25˚C and 50% humidity on a 12-hour light–dark cycle using standard Bloomington Drosophila Medium (Nutri-Fly)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After 5 days (young) and 70 days (old), brains were dissected and RNA was purified with TRIzol.
PolyA+ RNA was purified using Dynabeads Oligo(dT)25 (Thermo Fisher) beads and constructed into strand-specific libraries using the dUTP method . UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics, MA), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual-indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter, CA) and quantified by qPCR before and after amplification. Sequencing was performed in paired-end mode on a NextSeq 500 (Illumina, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
flyBrain.d70.b4
|
| Data processing |
RNA-seq reads were mapped to the Drosophila melanogaster assembly BDGP6 pre-indexed with transcript models from Ensembl 87 using STAR 2.5.0b with default parameters except --alignIntronMax set to 10,000
Aligned reads were assigned to gene models using the summarizeOverlaps function of the GenomicRanges R package
Reads per kilobase per million (RPKMs) were calculated with a slight modification, whereby only reads assigned to annotated protein-coding genes were used in the denominator, to minimize batch variability due to different amounts of contaminant ribosomal RNA
Genome_build: BDGP6
Supplementary_files_format_and_content: count table
|
| |
|
| Submission date |
Apr 30, 2020 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bonasio
|
| Street address |
3400 Civic Center Blvd - SCTR 9-111
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE149667 |
RNA-seq in old and young Drosophila brains |
| GSE149668 |
Social reprogramming in ants induces longevity-associated glia remodeling |
|
| Relations |
| BioSample |
SAMN14783425 |
| SRA |
SRX8218204 |
