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| Status |
Public on Oct 06, 2023 |
| Title |
Pupal Brain, WT, Rep. 4 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Brain
developmental stage: pupal
genotype: AspT25/+
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| Treatment protocol |
None
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| Growth protocol |
Animals were maintained at 25C on cornmeal-agar; brains were dissected in fresh SF900 cell culture media.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol prep, DNAse Treatment (Turbo DNAse)
Per Novogene's polyA enrichment library preparation protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing reads were trimmed and filtered using FastQC and Cutadapt with length cutoff of 20 nt
reads were mapped to the Drosophila melanogaster reference genome (dm6) using the RSubread package
Gene expression levels were estimated using FeatureCounts software with default settings
Differential gene expression (DGE) analysis was performed using the EdgeR Bioconductor package, filtering for CPM <1
Genes with a logF.C. ≥ 0.5/≤-0.5 and an adjusted P-value ≤0.05 were assigned as differentially expressed
Assembly: dm6
Supplementary files format and content: tab delimited text file includes raw counts for each sample from FeatureCounts
Supplementary files format and content: tab delimited text file includes logFC, logCPM, F, Pvalue, and FDR for each genotype comparison computed using EdgeR
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| Submission date |
Oct 02, 2023 |
| Last update date |
Oct 06, 2023 |
| Contact name |
Todd Schoborg |
| E-mail(s) |
todd.schoborg@uwyo.edu
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| Phone |
3073142115
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| Organization name |
University of Wyoming
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| Department |
Molecular Biology
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| Street address |
1000 E. University Ave, Department of Molecular Biology, #3944
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| City |
Laramie |
| State/province |
Wyoming |
| ZIP/Postal code |
82071 |
| Country |
USA |
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| Platform ID |
GPL25244 |
| Series (1) |
| GSE244463 |
Identifying new cellular mechanisms of MCPH5 |
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| Relations |
| BioSample |
SAMN37652143 |
| SRA |
SRX21971205 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7816410_featureCounts_on_PBWTD_1_2_Counts.tabular.txt.gz |
75.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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