|
| Status |
Public on May 15, 2024 |
| Title |
sh-R41, Male infected, 0 hour, replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
whole fly
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole fly
cell line: Male
genotype: w/Y; Actin-Gal4/+; UAS-sh-circ_ATP8B/+
treatment: newly emerged flies that have been kept in molasses formulation food at room temperature for 4-7 days
|
| Treatment protocol |
Newly hatched male and female flies of appropriate genotypes were collected and kept in fresh food vials for 4-7 days prior to RNA extraction.
|
| Growth protocol |
Flies were maintained at room temperature with standard fly food (molasses formula).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Invitrogen).
Total RNA samples were subjected to cDNA library construction using illumina kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adaptor sequences and low-quality reads (those with an average quality score < 20) were removed from the paired-end raw data using Trim-galore (version 0.4.4).
The resulting cleaned reads were aligned to the Drosophila melanogaster (dm6) reference genome using the STAR splice-aware aligner (version 2.6.0c) with default parameters.
Ambiguous reads mapping to multiple regions in the genome and reads with a MAPQ score less than 10 were discarded.
Subread featureCounts (version 2.0.1) was then utilized for gene quantification, employing the FlyBase r6.40 gene annotation.
Genes without read counts in all samples were excluded from subsequent analysis.
Assembly: dm6
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text file include RPKM values for every gene and every sample
|
| |
|
| Submission date |
Nov 27, 2023 |
| Last update date |
Jul 11, 2024 |
| Contact name |
Rui Zhou |
| E-mail(s) |
rzhou13@jhmi.edu
|
| Organization name |
Johns Hopkins University
|
| Street address |
REB 4130, 501 6th Ave S
|
| City |
St Petersburg |
| State/province |
FL |
| ZIP/Postal code |
33701 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (2) |
| GSE248665 |
The circular RNA circ_ATP8B regulates ROS production and antiviral immunity [RNA-Seq] |
| GSE248667 |
The circular RNA circ_ATP8B regulates ROS production and antiviral immunity |
|
| Relations |
| BioSample |
SAMN38450725 |
| SRA |
SRX22651837 |
