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| Status |
Public on Aug 13, 2024 |
| Title |
Upf1, cycle9, rep3 |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: embryos
developmental stage: cycle 9
genotype: Upf1
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| Growth protocol |
Fly stocks were maintained by standard methods and grown at 25°C. Embryos were collected on apple-juice agar plates smeared with yeast paste.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from sorted embryos using TRIzol reagent (Thermo Fisher Scientific).
Samples were poly(A) selected and libraries were prepared using TruSeq Library Prep Kit (Illumina) following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
RWUpf_D
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| Data processing |
Adapter sequences were trimmed from paired-end 150-nucleotide raw reads followed by trimming low-quality bases from the 3’ end of reads based on a minimum Phred quality score of 15.
Reads of less than 60nt were removed, as were reads mapping to mtRNA, tRNA, and rRNA.
STAR (v2.5.3a) was used to map the reads to dmel_r6.22_FB2018_03.
Mapped reads were counted using RSEM (v1.3.0). The resulting outputs were analyzed in R (v4.2.1) using the edgeR package (v3.40.2) to find differentially expressed genes and transcripts.
Low abundance genes and transcripts were filtered out by setting min.count=30 and min.total.count=30 in filterByExpr function in the edgeR package, removing genes and transcripts with < ~2 counts per million mapped reads.
Assembly: dmel_r6.22_FB2018_03 (BDGP6.22.96)
Supplementary files format and content: tab-delimeted text files include raw counts for each sample
Supplementary files format and content: tab-delimeted text files include TPM values for each sample
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| Submission date |
Apr 15, 2024 |
| Last update date |
Aug 13, 2024 |
| Contact name |
Mohammad Marhabaie |
| Organization name |
Nationwide Children's Hospital
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| Street address |
700 Children's Dr
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| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43205 |
| Country |
USA |
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| Platform ID |
GPL21306 |
| Series (1) |
| GSE264028 |
Widespread regulation of the maternal transcriptome by Nanos in Drosophila |
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| Relations |
| BioSample |
SAMN40974642 |
| SRA |
SRX24267672 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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