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| Status |
Public on Nov 08, 2023 |
| Title |
Whole_RNA_DD8F1-2 |
| Sample type |
SRA |
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| Source name |
Male adult whole flies
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w1118
parental photoperiod: Consistent darkness
parental age after eclosion: 8 days
replicate: 2
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| Treatment protocol |
To investigate the mRNA profiles of w1118 F1 generation under the influences of parental photoperiods and natural aging, we collected the eggs from 8- and 23-day-old flies, colonized them under DD until 3 days after eclosion, and sampled these bulk 3-day-old male adult whole flies for poly-A RNA-seq (BD8F1, BD23F1, DD8F1, and DD23F1).
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| Growth protocol |
We collected the eggs oviposited by 3-day-old Drosophila melanogaster w1118 adults which were colonized under the photoperiodic cycles of 12 h white fluorescent light: 12 h darkness (LD) after eclosion. These eggs were grown on standard mediums (comprised of 80 g cornmeal, 125 g sucrose, 16 g yeast, and 5 g agar/L) under the photoperiodic cycles of LD until one day after eclosion.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were isolated and dissolved in RNase-free water after the bulk samples had been homogenized in 0.5–1 mL TRIzol AG RNAex Pro Reagent (#AG21102, Accurate Bioeng. Co., Ltd., Hunan, China) with glass beads using a homogenizer.
Poly-A RNAs were purified from the extracted total RNAs using Dynabeads™ Oligo(dT)25 (#61002, Invitrogen, CA, USA) and were further fragmented as ~350 nt fragments using NEBNext® Second Strand Synthesis (dNTP-Free) Reaction Buffer (#B6117S, New England BioLabs, MA, USA). Strand-specific sequencing libraries were conducted using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, New England BioLabs) according to the manufacturer's protocols including first- and second-strand cDNA synthesis, adaptor ligation, and library amplification with index sequences.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Photoperiod: Consistent darkness; Parental age after eclosion: 3 days
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| Data processing |
After removing adaptors and low-quality bases by fastp (version 0.20.1), the resulting reads no less than 50 bp were mapped to the Drosophila melanogaster reference genome (FB2021_02) released by FlyBase database (http://flybase.org/).
The featureCounts program within SourceForge Subread package (version 2.0.2) was used for counting the reads that mapped to genes.
The genes with an average read count less than 10 in any group or lacking read count in any replicate were primarily filtered.
R package DESeq2 (version 1.30.0) was used for the identification of differentially expressed genes (DEGs) by setting false discovery rate corrected P-value (FDR) < 0.05 and fold change >= 2 as the thresholds of significance (Supplementary Table S2), and the read count normalization across samples by size factors.
t-SNE dimension reduction analysis was performed using R (version 4.0.3) package Rtsne (version 0.15); heatmap was generated using R package pheatmap (version 1.0.12); common and unique DEGs were visualized in a Venn diagram generated using R package VennDiagram; volcano plot was generated using R package ggplot2; GO (Gene Ontology) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for the DEGs were performed using either Metascape (version 3.5) (https://metascape.org/) or R package clusterProfiler (version 3.18.1); Gene set enrichment analysis (GSEA) software (version 4.2.0) was used for determining the statistical significance of priori defined gene sets.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited text file (.txt) includes raw read counts for the RNA-seq data of w1118 F1 generation male adult whole flies.
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| Submission date |
Feb 24, 2022 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Xiaoyun Wang |
| E-mail(s) |
wang_xiaoyun@gibh.ac.cn
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| Organization name |
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
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| Department |
Infection and Immunity
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| Street address |
190 Kaiyuan Avenue, Huangpu
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
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| Platform ID |
GPL25244 |
| Series (2) |
| GSE197382 |
5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila [RNA-seq whole] |
| GSE197397 |
5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila |
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| Relations |
| BioSample |
SAMN26232779 |
| SRA |
SRX14279421 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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