|
| Status |
Public on Jun 30, 2023 |
| Title |
w1118 head RNA, control, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: head
genotype: w1118
age: 3-4 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 20 fly heads per sample using TRI reagent. Isolated RNA was stored in 80% ethanol. |RNA was quantified using Qubit 3.0. Further RNA integrity was checked on high sensitivity tape (Agilent TapeStation 2200). Samples with RIN number >8.5 were selected for library construction.
Three w1118 and three Ssdp[2082-G4] /+ samples were used to prepare 100bp paired sequencing library using the TruSeq Stranded mRNA Library prep kit and >40M read per sample were sequenced on an Illumina NovaSeq6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CTL-1
|
| Data processing |
The dm6 was used as a reference Drosophila genome. Bowtie2 aligner was used to paired-end reads to the reference transcriptome. Known genes and transcripts were assembled with StringTie based. After assembly, the abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample. DEG (Differentially Expressed Genes) analysis was performed on a comparison pair (SSDP_vs_CTL) using DESeq2, genes were selected if they satisfied |fc|>=1.5 & nbinomWaldTest raw p-value<0.05 conditions in a comparison pair (3 SSDP_vs_ 3 CTL).
Assembly: dm6
Supplementary files format and content: Microsoft Excel file, contains significant genes with satisfies |fc|≥1.45 & raw.p<0.05 conditions in at least one of total comparison pairs.
|
| |
|
| Submission date |
Dec 07, 2022 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Safa Salim |
| E-mail(s) |
safasalim1125@gmail.com
|
| Organization name |
Hamad Bin Khalifa University
|
| Street address |
21, Kuwari Building, Khaleel Bin Ahmed Street, Umm-Ghuwailina
|
| City |
Doha |
| State/province |
Qatar |
| ZIP/Postal code |
4020 |
| Country |
Qatar |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE220311 |
Ssdp influences neurodevelopment and autism-like behaviors in Drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN32092073 |
| SRA |
SRX18524366 |
